Lecture 1A: Introduction to Microbial Physiology and Prokaryotic Cell Structure Flashcards
What is microbial physiology?
- Study of how microbial cell structures, growth, and metabolism work in microorganism.
- Study of microbial cell functions which includes the study of microbial growth, microbial metabolism, microbial cell structure .
- Structure-function relationships in microorganisms, especially how microbes respond to their environment.
- Foundational to advanced or applied fields such as metabolic engineering and functional genomics
Prokaryotic cell structure
- Cell morphology
- The small world
- The Cell Membrane and Wall
- 3A: cytoplasmic membrane
- 3B: Bacterial Cell Walls: Peptodoglycan - Cell Surface structures and inclusions
What are the 6 cell morphology?
- Coccus
- Rod
- Spirillum
- Spirochete
- Budding and appendaged
- Filamentous
typically DOES NOT predict physiology, ecology, phylogeny or other properties of prokaryotic cell.
Morphology
Morphology typically DOES NOT predict ____, _____, ______ or other properties of prokaryotic cell.
physiology, ecology, phylogeny
may be ____ ___ involved in setting the morphology
selective forces
3 example of selective forces involved in setting the morphology
- optimization fornutrient uptake
- swimming motility in viscous environments or near surfaces
- gliding motility
What is the size range for prokaryotes
0.2 um to >700 um in diameter
What are the two microorganism that are exception the rule of the size range for prokaryotes
- Epulopiscium fishelsoni
- Thiomargarita namibiensis
Width and length of most cultured rod-shaped bacteria
between 0.5 and 4.0 µm wide and <15 µm long.
What is the size range for eukaryotic cells
0.2 to >600 um in diameter
On the average, what is the limit of resolution of human eye?
0.1 um
It is necessary for growth rates and evolution
Surface-to-volume ratios
Surface-to-volume ratios is necessary for what?
Growth rates and evolution
ADVANTAGES TO BEING SMALL:
- More surface area relative to cell volume than large cells
- Support greater nutrient and waste product exchange per unit cell volume
- Tend to grow faster than large cells
- Mutation leads to faster evolution
- Prokaryotic cell has faster adaptive state
More surface area means more what
Cell membrane
Why having more cell membrane is advantageous
Much faster nutrient uptake
Why high volume with small surface area is disadvantageous
Cells cannot cope because of the lower rate of nutrient uptake resulting in slower uptake of nutrients than the metabolism.
What will happen if the metabolism is too fast?
cell cannot cope since cell membrane is not enough to take up and transport nutrients needed by the cell
High volume = high ____ requirement
Energy
Lower limits of cell size
- Cellular organisms <0.15 µm in diameter are unlikely
- Need volume to house proteins, nucleic acids, ribosomes, and so on
- Open oceans tend to contain small cells (0.2 - 0.4) known as “ultramicrobacteria”
- Genomes are highly streamlined, missing functions that must be supplied by other microbea or hosts (plants and animals)
What do you call the small cells ( 0.2-0.4 um) found in open oceans
ultramicrobacteria
parasite that depends completely on the host for its habitat, nourishment, reproduction, and survival
Obligate parasites
In what habitat do cells typically appears smaller in size than those of comparable higher nutrient habitats
- in low-nutrient habitat (oligotrophic) in marine plankton
T or F: microbial cells in terrestrial is larger than in marine waters due to the rich environment (soil)
True
there may be loose relationship between cells ____ and ambient ___ concentration
Size ; nutrient
It has greater surface
Smaller cells
postulated to be adaptive for low nutrient environments however small cell size does not necessarily imply adaptation to oligotrophic lifestyle
Smaller cells
Example of microorganism where there is a relationship between minimum size and environment
- new verrucomicrobiales
- Nanobacteria
3.symbiotic and parasitic bacteria
new verrucomicrobiales isolates grow well and maintain small cell size under what condition?
relatively high nutrient growth condition
isolates grow well and maintain small cell size under relatively high nutrient growth condition
new verrucomicrobiales
Nanobacteria dwell (and are cultivated) in a what kind of environment
Relatively nutrient-rich environment
dwell (and are cultivated) in a relatively nutrient-rich environment, yet maintain their small cell dimensions.
nanobacteria
are known that have reduced physiological capacities and reduction(?) sizes
symbiotic and parasitic bacteria
*Surrounds cytoplasm
*Separates it from environment
*Main function: selective permeability (nutrients transported in and waste products out)
Cytoplasmic membrane
Cytoplasmic membrane is surrounded by what
cytoplasm
what is the main function of cytoplasmic membrane
selective
permeability (nutrients transported
in and waste products out)
What is the general structure of bacterial cytoplasmic membrane
phospholipid bilayer containing embedded proteins.
Bacterial cytoplasmic membrane contains what
both hydrophobic and hydrophilic components
Hydrophobic component of cytoplasmic membrane is composed of what
Long chain fatty acids
Hydrophilic component of cytoplasmic membrane is composed of what
glycerophosphate portion with functional group
What is the linkage in phospholipids of bacteria
Ester linkages
- Thinner than cell wall
- 8-10 nm
Bacterial cytoplasmic membrane
- mostly extremophile
Archaea
Some species of bacteria is strengthened by what
hopanoids (sterol-like molecules)
important sterol component of cell and mitochondrial membranes in fungi
ergosterol
Archaea has embedded proteins including:
- integral membrane proteins (significantly embedded)
- peripheral membrane proteins (loosely attached)
What linkages is in phospholipids of Archaea
Ether linkages
What linkages is in the phospholipids of bacteria and eukarya
Ester linkages
Instead of fatty acids, what is the archaeal lipids composed of?
Isopheres
What are the major lipids of archaeal membrane
- Phosphoglycerol diethers with phytanyl C20 side chains
- Diglycerol tetraethers with biphytanyl C40 side chains
The major lipids of archaeal membrane can form lipid ____
monolayer
lipid monolayer is usually observed in what type archaeal organism?
Thermophilic Archaea
Other type of archaeal membrane is found in?
Crenarchaeol
- has multiple bonds
- melts longer at high temperature
crenarchaeol
Give the 3 main function of cytoplasmic membrane
- permeability barrier
- protein anchor
- energy conservation and consumption
- Must be transported
- need the assistance of transport proteins
Polar and charged molecules
accumulate solutes against the concentration gradient.
Transport proteins
- holds transport proteins in place
protein anchor
generation of proton motive force
energy conservation and consumption
In simple diffusion, the movement of solute is driven by what
Concentration gradient
Principle of simple diffusion
Rate of solute entry increases as the external concentration of the solute also increases (assuming the membrane is permeable to solute)
States that the rate of diffusion of a substance is directly proportional to the concentration gradient
Fick’s law of diffusion
In simple diffusion, the steeper concentration gradient =?
the faster the rate of diffusion
What is the principle of transporter saturated or high affinity transporter
there is a linear increases as the external concentration increases (as long as transport protein or the channels are not saturated)
Example of transporter saturated (high affinity transporter)
Facilitated diffusion
Facilitated diffusion move through what
Solutes move through membrane proteins (channels or carrier proteins)
What will happen to rate of entry once the protein channels or carriers are saturated
Decreases
Low rate of entry levels would result in what
plateau even with high external concentration
Key point of Transporter saturated (high affinity transporter)
there is an initial increase in the rate of entry with increasing external concentration but the rate reaches at the maximum when all available transport sites are occupied
low affinity transporter
Example
Active transport
low affinity transporter
requires what
energy in the form of ATP
Whhat influences the rate of solute entry in low affinity transporter?
- external concentration
- energy available
- number of active transporters.
At low concentrations, what happens to the active transport rate
Active transport rate increases as the external concentration rises
At much high concentration, what happens to the active transport rate
may become limited by factors like ATP availability or transporter capacity
T or F: Active transport doesn’t plateau immediately, it starts to slow down.
T
Key point of low affinity transporter
external concentration affects the transport rate but energy is required and transporter may be saturated or work at maximum capacity
Species of Bacteria separated into two groups is based on what
Gram stain
T or F: Gram-positives and gram-negatives have the same cell wall structures.
F
What is the structure of Gram-negative cell wall
- Lipopolysaccharide
- peptidoglycan
serves as an outer membrane
LPS
What type of carbohydrates is sticking out in outer membrane
of gram negative bacteria
oligosaccharides
Structure of gram positive cell wall
one layer of peptidoglycan
Structure of Peptidoglycan
- rigid layer that provides strength
- typically composed of alternatively modified glucose
- Amino acids
link N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM) in peptidoglycan
B-1,4 linkages
What are the alternatively modified glucose that the peptidoglycan of bacteria are typically composed of
N-acetylglucosamine (NAG)
N-acetylmuramic acid (NAM)
bacterial peptidoglycan is typically composed of 4 amino acids, namely:
- L-alanine
- D- alanine
- D- glutamic acid,
- either L-lysine ordiaminopimelic acid (DAP)
Amino acid that is unique only to bacteria
DAP
The amino acid is in __-form in prokaryotes and __-form in eukaryotes
D-form = prokaryotes
L- form = eukaryotes
Connection from one peptidoglycan to the next peptidoglycan is called
interbridges or tetrapeptide bridges
- can destroyed the peptidoglycan
- cuts at the beta 1,4 linkages
Lysozyme
How many distinct peptidoglycans have been described
100+
NAG and NAM varies in where
carbon number 3
perpendicular to the peptidoglycan molecule
Tetrapeptide bridges
Is a gram negative
Escherichia coli
Is a gram positive
Staphylococcus aureus
What does peptide bonds connect
M-M
Glycosidic bonds connect what
M-G-M
do not attack the tetrapeptide bonds, it attacks glycosidic bonds
Lysozyme
How many % of gram positive cell wall is peptidoglycan
up to 90%
- The other 10% of gram positive cell wall
-Acidic substance - generally negatively charged
- teichoic acids
What is the reason why cell wall attracts basic dyes
Because teichoic acids are generally negatively charged so they kind of confer a negative charge to the cell wall
Teichoic acid bind what kind of metal ions prior to transport
divalent metal ions (ex: Ca+2 and Mg +2)
- it is when teichoic acid is covalently bound to membrane lipids
Lipoteichoic acid
Example of teichoic acid in Gram positive
Ribitol teichoic acid
Few example of prokaryotes lack cell walls
- mycoplasma
- thermoplasma
- have tough cytoplasmic membranes (ex: steroids or lipoglycans)
group of pathogenic bacteria related to gram-positives
mycoplasma
- Archaea
- No cell wall - have additional components in cell membrane to make cell membrane tougher
thermoplasma
enhances the integrity of membrane
Lipoglycans
____ amount of total gram negative cell wall contains peptidoglycan
Small amount
Most of gram negative cell wall is composed of what
outer membrane or the Lipopolysaccharide layer
acts as barrier against antibiotics and other harmful agents
Outer membrane
LPS are consists of?
- Core polysaccharide
- O polysaccharide
- Lipid A
What replaces most of phospholipids in outer half of outer membrane
LPS
What makes the outer membrane different from cell membrane?
LPS replacing most of phospholipids in outer half of outer membrane
- endotoxin
- the toxic component of LPS
- Never released
- Natural part of gram negative
lipid A
a sugar unique to bacteria
KDO
- consist of 7 carbon sugar
- same to all species
Core polysaccharides
- repeating units
- its number is where gram negative species to species differs
O-specific polysaccharides
space located between cytoplasmic and outer membranes
Periplasm
transmembrane protein channels for entrance and exit of solutes
Porins
connects the outer membrane to peptidoglycan
Braun lipoprotein
T or F: All archaeal Cell Walls
False
T or F: not all cell wall of Archaea is Pseudomurein
True
Archaeal cell walls has no ____
peptidoglycan
Archaeal Cell Walls does not have peptidoglycan but has what
Pseudomurein
Pseudomurein is found in
cell walls of certain what kind of Archaea
methanogenic Archaea
Pseudomurein is polysaccharide similar to what
Peptidoglycan
What are Pseudomurein composed of
N-acetylglucosamine (NAG) and N- acetyltalosaminuronic acid (NAT)
What kind of bond do archaeal cell wall have
B-1,3 glycosidic bonds
What is the amino acid of Archaeal cell wall
L-stereoisomer
Cannot be destroyed by lysozyme and penicillin
Pseudomurein
Pseudomurein is insensitive to what
lysozyme and penicillin
- most common cell wall type of Archaea
S-layers
S-layers are consist of what
protein or glycoprotein
Structure of S-layers
paracrystalline structure
T or F: S-layers are always outermost layer
True
T or F: in many organisms, S-layers present in addition to other cell wall components, usually polysaccharides
T
They are not considered part of
cell wall because these
do not confer significant
structural strength
Capsules and slime
layers
Capsules and slime
layers are made up of what
polysaccharides ( maybe thick or thin,
rigid or flexible)
if tightly
attached, tight matrix:
visible if treated with
india ink
capsule
loosely
attached, easily
deformed (Leuconostoc)
slime layer
They assist in attachment to
surfaces
Capsules and slime
layers
Capsules and slime
layers have a role in what?
development and
maintenance of biofilms
Virulence factors of Capsules and slime
layers
protect against
phagocytosis
*
What do capsules and slime
layers prevent
dehydration/desiccation
- Filamentous
protein structures
about 2-10 nm
wide
Fimbriae
Fimbriae Enable organism to
stick to ___ or form ____
stick to surface or
form pellicle
thin
sheets of cells on a
liquid surfaces
pellicle
typically longer and
fewer (1 or few)
found per cell than
fimbriae
Pili
2 types of pili
- Conjugative/sex
pili - Type IV pili
Function of conjugative/sex pili
facilitate genetic
exchange between cells
(conjugation)
Function of type IV pili
adhere to host
tissues and support
twitching motility
Example of type IV pili
Pseudomonas
and Moraxella
cell surface structure usually associated with Archaea
Hamus/hami
Where is hamus/hami found
SM1 archaeal
group only
Hamus/hami is an acrhaeal “______ ____” assist in surface
attachment, forming
biofilms
“grappling
hooks
Hamus/hami is an archaeal “grappling
hooks” that assist in what
surface
attachment, forming
biofilms
What do hamus structurally resemble
type
IV pili
hamus structurally resemble type
IV pili expect for what
barbed
terminus, which attaches
cells to surfaces or each
other.
What are the three cell surface structure
- Capsule and slime layer
- Fimbriae and pili
- Hamus (singular) /hami
What are the 4 cell inclusion
Polyphosphate granules
Sulfur globules
Carbonate minerals
Magnetosomes
inorganic
phosphate
*Polyphosphate
granules
elemental sulfur found in
periplasm, oxidized to
sulfate
Sulfur globules
Formed during the
endosporulation or
sporogenesis
Endospores
Endospores are formed during what
endosporulation or
sporogenesis
Endospore are highly what
- Highly differentiated
- Highly resistant to
heat, harsh
chemicals, and
radiation
Why endospore has survival structures
to endure
unfavorable growth
conditions
Endospore behave as dormant
structure as long as what
conditions remain
harsh or
unfavorable for
vegetative cell
T or F: there are
endospore that
remained dormant
for hundred of
year
T
dormant stage of
bacterial life cycle
Endospores
endospore is ideal for what
dispersal via
wind, water, or animal
gut
Where is endospore present
only in some
gram-positive bacteria,
(e.g., Bacillus and
Clostridium)
vegetative cell
converted to what
nongrowing
(dormant),
heat-resistant, light
refractive structure
Formation of endospore only occurs when?
growth ceases due
to lack of essential
nutrients such as
carbon or nitrogen
What sre the 3 process of endospore
Activation, germination, outgrown
Activation process
heated for
several minutes at
elevated but sublethal
temperature but high
enough to activate
endospore
It must be
present (just like
an activated
imbibition) during activation
Water
Its is the
first step in germination and is
defined by a rapid
increase in the
uptake of water by
a seed
imbibition
Process of germination
rapid
(minutes), loss of
refractility and loss of
resistance to heat and
chemicals
Process in outgrown
swelling
from water uptake and
synthesis of RNA,
proteins, and DNA
Layers of endospore
exosporium (outermost),
spore coats, cortex, core
Where is DNA protected in the layers of endospore
Core
Endospore contains what
dipicolinic acid
(DPA)
is partly
responsible for the
resistant nature of
endospore
because it
contributes the
highly dehydrated
nature of
endospore
dipicolinic acid
(DPA)
What is water to the cell
universal solvent in
cell
Endospore is enriched in what
Ca2+
Responsible for
highly dehydrated
nature of
endospore due to
its ability to
intercalate DNA
Ca2+ DPA complex
What is core made up of
contains small
acid- soluble spore
protein (SASP)
small
acid- soluble spore
protein (SASP) function
carbon
and energy source
outgrowth
- complex series of
events - 200+
spore-specific genes
sporulation cycle
Diversity and
phylogenetic aspects of
endospore
- Nearly 20 genera
form endospores. - diverse
physiologies
master sporulator
regulator protein
SpoO A
T or F: ALL species produce 1
endospore
F
