Topic 2 Flashcards
Difference between prokaryotes and eukaryotes (2)
- Prokaryotes are smaller in size (bacteria cell size roughly equivalent to Mitochondria)
- Eukaryotes have membrane bound organelles that compartmentalize cells. Prokaryotes have cell wall/cell membrane –> compartmentalization is closed off.
Most bacteria cell are _______ micro-metres in length.
0.5 to 10
(Largest Prokaryote: Epulopiscium fishelsoni
Smallest Prokaryote: Mycoplasma pneumonia)
Why does surface area to volume ratio matter in terms of cell size and cell growth?
SA/V ratio affects how quickly cells exchange nutrients and waste into their environment. Small cells can grow/reproduce more quickly–> use less time/energy to replicate cells.
Shape of prokaryotes are determined by what factors? (4)
In no particular order:
- cell wall structure
- cell growth
- division mechanisms
- cell differentiation
Know your morphology vocab kidzz! (6 important terms)
- Coccus (sphere)
- Rod
- Spirillium (worm-like)
- Spirochete (S-shape/wavy hair shape)
- Stalk and Hypha (look like ladles)
- Filamentous
Name three types of Cocci: spheres and examples!!
- Staphylococci: cluster of cocci –> ex: Staphyloccus aureus, in human microbiota and opportunistic pathogen
- Dippococci: pairs of cocci –> ex: Neisseria gonorrhoeae, STD gonorrhea
- Streptococcus: chains of cocci –> ex: Streptococcus pyogenes, strep throat
Note: You can also have a single free-floating sphere —> ‘coccus’
Name Bacilli rod example:
Salmonella enterica –> food positioning and can cause typhoid fever
Example of Vibrio: Comma shaped:
hint: Neha’s pun ;)
Vibrio cholerae; human pathogen that can cause diarrhea and hydration
Name example of Helical shape:
Spring shaped
Helicobacter pylori; human stomach, cause of stomach ulcers, stomach cancers
Example of Spirochetes (Long spirals):
Borrelia burgdorferi; bacteria pathogen causing Lyme diseases by ticks
Example of Appendaged/Budding:
Caulobacter crescentus; study bacterial cell cycle, asymmetric cell division
Example of Filamentous Shape:
Noodles shaped!
Chloroflexus aurantiacus; photosynthetic bacteria don’t produce oxygen
How can cell shape affect aspects of day to day life? (5)
o Nutrient access/uptake (surface:volume ratio)
o Motility
o Attachment to surfaces
o Formation of biofilms
o Interactions with other microbes and/or eukaryotic host cells
Monomorphic vs Pleomorphic:
hint: mono means single; p stands for pleural
Monomorphic: adopt one shape; observed in most pure cultures of bacteria
Pleomorphic: multiple different morphologies for same bacterium, adopt multiple morphologies
What causes different morphologies/changes of morphology? (3)
o Differentiation into different cell types or spore formation –> cell program change
o Altered morphology in response to environmental stress
o Altered morphology due to mutation
What’s special about Arthobacter crystallopoietes?
Its pleomorphic!
Rod shapes during fast/logarthmic growth
Coccus during slow/ no growth
Major structures of the Cell Envelope: (4)
- Cytoplasmic membrane
- cell wall
- outer membrane
- S-layers
Roles of the Cell Envelope: (4 main ones)
o Maintains barrier with environment
o Protects cell from stress
o Allows transport of nutrients into cell and waste out of cell
o Energy conservation/production
Difference between Gram-negative and Gram-positive cell envelope?
Gram positive:
thick cell wall, no outer membrane, different/smaller periplasmic space
Gram negative: (think of a sandwich - has 2 membranes)
thin cell wall, outer membrane, has another cell membrane, periplasmic space b/w the two membrances
Explain the three functions of cytoplasmic membrane:
- Permeability barrier: prevents and functions as a gateway for transport of nutrients, waste in/out of cell
- Protein anchor: site of proteins that participate in transport, chemotaxis, bioenergetics
- Energy conservation: Site of generation and dissipation of proton motive force ( this basically saying that it helps pump photons against the energy/photon gradient)
Hydrophilic vs Hydrophobic:
Hydrophilic: “water loving” molecules; Ionic
and/or polar.
Hydrophobic: “water fearing” molecules; nonpolar.
Which parts of the cytoplasmic membrane are hydrophilic and hydrophobic?
Hydrophilic: Backbone –> glycerol and phosphate (is conserved in both euk. and prok.)
Hydrophobic: Fatty Acid Tails –> E.g. unsaturated
fatty acids (contain double bonds = kinks) increase fluidity (decrease rigidity) of membrane.
What are the three proteins found in the cytoplasmic membrane?
- Peripheral membrane proteins –> only on one side of the membrane
- Integral membrane proteins (embedded in membrane)
- Transmembrane proteins (are
integral membrane proteins that pass all the way through membrane) –> runs from one side to another
Why does it mean when the Cytoplasmic membrane have “two faces”?
One side of cytoplasmic membrane faces the cytoplasm and the other faces outward (
periplasmic face).
Specific Topolgies!
2 faces of the cytoplasmic membrane are identical in respect to the phospholipids, but not identical cause the proteins in different direction make domains face different from one another.
Function of Cell Wall?
- prevent cells from bursting due to osmotic
pressure
-cell shape, rigidity
What is peptidoglycan?
lattice-like structure formed from
chains of glycans linked together by peptide bridges
Glycan Chains in Pepidoglycan? (MEMORIZE)
N-acetylglucosamine (GlcNAc, NAG) &
N-acetylmuramic acid (MurNAc, NAM)
connected by β(1,4) linkage (glycosidic
bond)
Peptide Bonds in Peptidoglycan’s? (MEMORIZE THE IMAGE ON SLIDE - MY INSTINCT SAYS IT MAY BE ON THE EXAM)
• Sequence can vary
• D-isomers: amino acids; L-isomers: proteins
• Crosslinks between position 3 (diaminopimelic
acid “DAP” – can be a lysine) and
position 4 (D-alanine)
Gram negative bacteria:
~1-3 peptidoglycan layers
~2-7 nm
Purpose of Interbridges in Gram + bacteria:
connect peptidoglycan layers (thicker than Gram - bacteria)
Purpose of Teichoic Acids in Gram + bacteria:
o Provide cell strength (ionic
interactions between metal ions)
o Help trap metal ions ex: Mg2+
o Barrier & attachment functions
What is Teichoic Acid?
Long polymers comprised of glycerol phosphate or ribitol phosphate with attached D-glucose and/or D-alanine
Role of Wall-associated proteins in Gram + bacteria:
cell adhesion
Ps: proteins can take part in covalent or non-covalent bonds with the cell wall
Gram staining influence on Gram positive bacteria?
thick layer of peptidoglycan is dehydrated – pores close and prevent escape of crystal violet dye – cells are stained purple
Gram staining influence on Gram negative bacteria?
decolorizing agent degrades outer membrane, thin/porous peptidoglycan layer does not retain purple stain. Cells appear pink due to safranin counterstain
Whats special about Mycoplasma pneumoniae?
Lacks cell wall due to minimal osmotic pressure in environment & has strong cell membrane
Three parts of Lipopolysaccharides (LPS)?
- lipid A (within membrane)
- core polysaccharide (sugar subunits connected to one another)
- O-specific polysaccharide (outermost component)
What’s lipid A?
- Hydrophobic tails anchor in outer membrane
- contains endotoxins –> immune system detects lipid A and sends message that bacteria was here
Note: mostly conserved from species to species
What’s O-specific polysaccharide?
o Polysaccharide comprised of diverse sugar subunits connected and branched in different ways
o Repeating combination of sugars with variable numbers of repeats
Note: it’s highly variable even within species!
Braun’s lipoproteins?
connect the outer membrane to cell wall
- produced by ribosome attached to lipids
- VERY abundant in Gram - cells
Porins in Outer Membrane:
- protein channels that serve as channels for entrance/exit (not impermeable to large molecules) of small molecules
- Can be specific or non-specific. Can be regulated
Functions of the outer membrane: (4)
- Provides mechanical strength to cell
-Soaks up or blocks
access to many molecules – important for antibiotic sensitivity - Protects cell wall
- Enables a substantial periplasmic space
What is the periplasmic space?
- Space between cytoplasmic/outer membranes of Gram negative bacteria
- Buffer between environment and cell
- Technically, cell wall is part of periplasmic space
Role of periplasmic space? (4)
o Break down macromolecules for uptake as nutrients
o High affinity binding protein for nutrients
o Detoxify harmful compounds
o Protein folding - disulfide bond formation
S-layers?
- Rigid/permeable monolayer of protein or glycoprotein that protect bacteria from bacteriophage or bacterial pathogens from host defences
Difference between capsule and slime layer?
Capsules are organized into a matrix and attached to the cell – slime layers
are loosely attached, less organized
Similarities between capsule and slime layer?
Hint: 3 similar functions
- cell adhesion
- protection from host immune system
- prevent dehydration
Conjugative pili?
transfer of genetic
material between bacterial using a pilus
bridge
Fimbria?
a pilus that mediates attachment to a surface or another cell
What molecules can cross freely across cytoplasmic membrane?
o Small uncharged, non-polar molecules
o E.g. - Dissolved O2, dissolved CO2, small alcohols/fatty acids
What molecules can not cross freely across cytoplasmic membrane?
large/charged molecules, ex: Na+/K+
Passive transport?
No energy needed for bringing molecules down concentration gradient.
-Simple diffusion, Facilitated diffusion (requires transporters)
Active transport?
need energy for uptake against concentration gradient
- Simple transport, ABC transporters, Group transport
Diffusion vs Osmosis?
Diffusion: The net from area of high concentration to area of low concentration
Osmosis: is the diffusion of water through a selectively permeable
membrane along its concentration gradient.
Facilitated Diffusion:
Diffusion of
molecules across the membrane using
membrane protein that acts as a channel. Can be nonspecific, specific, regulated.
Ex: Porins!!
Where does energy needed for Active Transport come from?
stored chemical energy (e.g. ATP hydrolysis) or from
transporting another
molecule along its concentration gradient (coupling)
Similarity b/w Symporters and Antiporters?
use proton motive force to power the transport of a different molecule against its
gradient
Difference b/w Symporters and Antiporters?
Symport: Both molecules travel same direction
Antiport: One molecule in, the other out
What is the main purpose of the Sodium Proton Antiporter?
– pH (and Na+) homeostasis!
- Expel Na+ from cell under high salt conditions
- Lower pH of cell under alkaline conditions
Lac permease symporter?
uptake of lactose and
disaccharides into
the cell through Proton motive force
What is Group Translocation?
- active transport
- Transported substance is bound by a transporter and is chemically modified during transport
- ex: Phosphorylation of sugar molecules
What are ABC transporters?
-active transport
- ATP binding cassette (ABC transporters) use
ATP to power the transport of substances across
the cytoplasmic membrane
Role of Periplasmic Binding Proteins?
to capture their ligand within the periplasm
Explain Vit B12 Transport?
- ABC transporter
- OM barrel protein BtuB binds B12 with high affinity, transports across OM using energy from TonB complex (via proton motive force)
Define Motility:
The ability to propel your own movement
Flagellum?
- a long, thin filament that acts like a propeller
- rotated using a motor that is anchored in the cell envelope
Peritrichous Flagellum?
many across pole/body
Monotrichous/ Polar Flagellum?
single at one pole
Lophotrichous Flagellum?
many, all at one pole
Amphitrichous Flagellum?
Both poles
Atrichous Flagellum?
No flagella at all
Direction of Peritrichous Flagellum?
CCW: Longer “runs” - cell moves forward
CW: Short “tumbles” – bundle falls apart – bacteria tumbles, starts new random orientation/direction
CCW –> CW: dictates direction of movement
Reversible Flagellum vs Unidirectional Flagellum?
Reversible flagellum: rotation in opposite
directions reverses direction of movement
Unidirectional flagella: rotation stops/starts; Random movement during “stops” change direction of bacterium
3 Segments of the Flagellum:
1) Filament: Long, thin propeller – drives movement
2) Hook: Adaptor that connects filament to the basal body
3) Basal body: Core of the structure. Powers rotation of filaments
What drives rotation in the flagellar motor?
proton motive force
Rings in the Central Rod and their roles:
MS ring (cytoplasmic membrane): rotates rod and hook and filament
P ring (peptidoglycan)/ L ring (outer membrane) :bearings (or bushings) to help rotation
C ring (cytoplasm): generating torque, switching motor direction, flagellin secretion
What does Gram + Flagellum lack?
lacks P/L rings – only contains C/MS rings
Flagellin?
The long filament that drives movement is made of thousands of copies of a single protein
- highly conserved in bacteria!
Type 3 Secretion System?
to export flagellin: a related system is used as a protein toxin injection system by certain bacterial pathogens
Synthesis of Flagellum?
MS/C RING –> STATOR –> P RING –> L RING–> EARLY HOOK –> CAP –> FILAMENT
(Made from inside —> out)
List 2 Variations of flagellar motility:
- use Na+ gradient to drive rotation
- Axial filament - rotation results in corkscrew motion of entire bacterium
Note: flagellar motility is highly regulated!
Chemotaxis:
Movement in the direction of gradients of increasing
or decreasing concentration to particular chemicals
Phototaxis vs Aerotaxis:
Phototaxis: Movement toward/away from light
Aerotaxis: Directed motility in response to O2
Twitching motility?
extend from cell –> attach onto surface –> retraction –> pull bacteria foward –> let go –> repeat
-type IV pilus
Note: like a grappling hook, would NOT be useful in liquids (aquatic bacteria)
Inclusions?
bodies or aggregates within the cell
Microcompartments?
protein shells than encase specific enzymes/metabolites/cofactors
that carry out specific metabolism
Which prokaryotes store carbon as lipids and form large granules?
- poly-β-hydroxyalkanoates (PHA)
- poly-βhydroxybutyric acid (PHB)
Polyphosphate Granules?
excess of phosphate – broken down
to produce nucleic acids/phospholipids
Sulfur Storage Granules?
oxidize reduced sulfur compounds for energy/CO2 fixation
Gas Vesicles?
-Protein structures that keep water/solutes
out, but allow gas in
-buoyancy!!
-ex: cyanobacteria
Carboxysomes?
concentrate enzymes involved in carbon fixation – increases efficiency and reduces unwanted side
reactions
Other functions of Microcompartments?
- protect cell against toxic/reactive intermediates/biproducts
Endospores?
Hint: ‘protective long storage mechanisms’
- highly differentiated, dormant cells that can
survive starvation - Gram +
- extremely resistant – heat, radiation, drying,
nutrient depletion, chemicals
Vegetative cells?
normal, metabolically active, growing/dividing cells
differentiate into endospores upon nutrient deprivation
What features are shut down in endospores? (3)
- enzymatic activity
- respiration rate
- Macromolecular synthesis
What features provide resistance/stability to endospores? (4)
- calcuim content
- dipicolinic acid
- water content
- small acid soluble spore proteins
Expand on the features provided resistance/stability? Like why they important?
Dehydration: water is < 25%
- increases resistance to desiccation, heat, chemicals – inactivates cell’s enzymes
Dipicolinic acid (DPA) – complexed with Ca2+ -dehydration process, binds/stabilizes DNA DPA structure
Small acid soluble proteins (SASPs) -
Bind DNA, protect it from damage
(UV, heat, denaturation, mutation). Also act as carbon/energy source during germination/outgrowth
Structure of Endospores?
Core is where DNA/ribosomes are housed
– will become the vegetative cell
Cortex – peptidoglycan layer
Two membranes – this “outer
membrane” – no LPS
Coat – protective protein layer comprised
of many different proteins
Major Events of Endospore Formation:
Endospore -> Germination -> Vegetative Cell -> Growth/Cell Division/ DNA replication ->Forespore contained in mother cell -> Engulfment ->Both inner/outer membrane formed -> Coat/Cortex formed -> Maturation (Ca2+, SASP, dipicolinic acid) -> Mother cell lysis -> cycle repeat
What do eukaryote cells have that’s cool and what do they do?
(its like a huge mansion compared to a cottage)
they have membrane bound internal structures that have their own functions creating complexity and organizations (like my mansion has a pool room and theatre)
NUCLEUS
separates genetic material from rest of the cell
trnsc/tranl uncoupled-ribosomes outside nucleus
proteins related to DNA must be translocated into nucleus
MITOCHONDRIA
universal among eukaryotes
energy centre of cell
own genomes, own ribosomes
evolved from alphaproteobacterium
GOLGI AND ER
Hint: post office Golgi
Modify and sort
Glycosylation
molecules packaged in vesicles and then trafficked
Know the other components of cells like cytoskeleton, vacuoles, lysosomes, chloroplasts, vesicles, cell wall,
However I feel like all of us have studied these multiple times so focus on memorizing stuff we don’t know
KEEP GOING WOOHOOOO
What eukaryotic cell do we use as a model
YEAST
LECA
last eukaryotic common ancestor
how many supergroups of eukarya are there ?
five, paanch, cinqo, cinq
who has more metabolic diversity? prokaryotes or eukaryotes?
prokaryotes
Algae
includes microbes and non-microbes, usually aquatic
hundreds of thousands species
Fungi
includes microbes and non-microbes, closely related to animals, non-motile
CHITIN (polysaccharide cell wall defining feature)
some fungi are human or pathogens
This fungal pathogen is the most common cause of a yeast infection
Candida albicans
Yeast convert carbohydrates into
CO2 and alcohol via fermentation
Amoeba (like the cute amoeba sisters)
single celled eukaryotic, inhabit freshwater and soil, amoebozoa is a diverse phylum of eukaryotes
what do amoeba use for locomotion (sounds like some kind of superpower)
pseudopods
Pseudopods
temporary projections that stick out and help move
Eukaryotic P-words
protist, plankton, parasite
protist
historical term used to describe eukaryotic microbe that is not a plant, animal or fungues
plankton (what’s the krabby patty recipe?)
drifters…they just drift in water or air
“so we drifting…wave after wave”
parasite
symbiotic relationship, some pathogens
T/F: Archaea domain shares a more recent common ancestor with Eukarya than Bacteria
True!
T/F: Bacteria are commonly known as extremophiles since they tend to live in extreme environments.
False. It’s Archaea that are extremophiles.
Similarities between Archaea and Bacteria?
- both prok.
- both usually single cell
- overall similar sizes/morphologies
Archaea cell membrane?
- ether-linked
- isoprenoid (different subunit compared to the lipid fatty acids in eukarya/bacteria)
- lipids contain side branches and rings
Some archaea produce __________phospholipids (a lipid monolayer) but the lipid tails are __________.
transmembrane; joined
joined lipid tails –> different from eukarya/bacteria
T/F: S-layers are present in both archaea and bacteria
True! BUT, they have different functions in each (covered in a diff. flashcard).
For majority of archaea, S-layers act as the ___________.
cell wall
In bacteria, S-layers act as ____________ structures.
supplementary
Archaea Cell Walls
- made of simple polymer: pseudomurein
- doesn’t have D-amino acids, different sugar linkages
- NAM replaced with N-acetyltalosainuronic acid
What is a hamus? (hami for plural)
hint: ‘grappling hook’ in archaea
in archaea, fixes cells to a surface to mediate biofilm formation
The archaellum
you guessed it: archaea + flagellum
- its like a flagellum BUT evolved separately from bacteria
- chemotactic
- driven by ATP hydrolysis (DIFFERENT from bacteria!!)
- built from inside out - Type IV pilus
T/F: Generally, archaea swim slower than bacteria.
Truee
An unusual archaea example: halophile with a long name
hint: i’m salty about how long this name is….
Haloquadratum walsbyi
- halophile –> lives in saturated salt lakes
- unique morphology: thin squares morphology ( like shreddies crackers)
- high Surface to Volume ratio
Asgard Archaea example
hint: add ‘archaeota’ at the end of an amazing marvel character’s name
LOKIarchaeota
- there’s also thorarchaeota, odinarchaeota etc. but not as important to know
Asgard Archaea Discoveries
- discovery bridged the gap between archaea and eukarya (get it…‘bridge’ like the Bifrost - k i’ll stop)
- in 2017, many asgard archaea discovered with new ‘eukaryotic functions’
- culturing asgard archaea finally happening in 2020 - after 12 years of efforts!
Asgard Archaea general facts
- Lokiarchaeota was found first
- found in anaerobic marine sediments
- contain eukaryotic - specific proteins (ex. vesicle trafficking)
