2. Structure and function Flashcards
1
Q
what are the 3 domains of life?
- what is the common ancestor? describe branching into the 3
A
- bacteria, archea, eukarya
- Luca! –> 2 branches: one becomes bacteria, the other separates into 2 (archaea and eukarya)
2
Q
what are 2 ways to grow microbes? –> purpose ish?
A
- in liquid or on agar plates (solid surface)
- goal: grow colonies –> so densely packed that we can see them with the naked eye!
3
Q
- what is colony morphology?
- what is a morphotype?
- characteristics are influenced by (2)
- why is it important to know morphology?
A
- characteristics of the colony produced by a species on solid agar: size, texture, color, etc
- morphotype: colony with specific characteristics –> ie 5 morphotypes on the picture in slides
*not an exact science! - influenced by the species (each species has a different morphology) + by the medium and the incubation conditions
- to know if you’re actually growing the right thing or if there’s contamination
4
Q
what are the 2 general function of cells?
A
- genetic function
- coded in DNA –> make something out of it
- DNA –> replication into more DNA OR transcription into RNA + translation by ribosome into protein/enzymes - catalytic function
- involved in metabolism
- enzymes are metabolic catalysts –> catalyze energy conservation reactions and synthesize macromolecules
5
Q
what are 3 properties of ALL cells VS 4 properties that some cells have
A
ALL CELLS:
1. metabolism: genetic and catalytic function –> convert E to do work
2. growth!
3. evolution: accumulation of mutations that confer new traits/properties, leading to new species –> important for adaptation
SOME CELLS:
1. motility (flagella and cilia)
2. differentiation (ie heterocytes in cyanobacteria have different functions than the rest of the cells)
3. formation of biofilm
4. virulence (ie: bacteria grows in macrophages –> infection of phagocytes)
6
Q
compare and contrast internal structure of cells
- bacteria and archaea
VS eukarya
A
BACTERIA AND ARCHAEA
*cytoplasmic membrane
*cytoplasm
ribosomes (free floating)
- nucleoid
- plasmid
- cell wall ()
**don’t have organelles/intracellular membranes
EUKARYA:
*cytoplasmic membrane
*cytoplasm
*ribosomes
- more complex organelles: mitochondrion, nucleus, nucleolus, rought ER, smooth ER, golgi apparatus, cytoskeleton, lysosome, centrosome, vacuole, peroxisome
7
Q
what is the nucleoid?
A
space where DNA is in bacteria and archaea –> their DNA is not delimited by a barrier but the nucleoid looks different on microscope
8
Q
what are the 3 functions of the membrane?
A
- PERMEABILITY BARRIER
- prevents leakage, transport systems, allow specific nutrients and waste to move across the membrane - PROTEIN ANCHOR
- about 50% of the membrane consist of proteins (sensors, transporters, enzymes, adhesins (allows cells to attach to a surface), etc.) - ENERGY CONSERVATION
- generation of proton motive force –> more portons on 1 side to create a gradient!
9
Q
- what is the cell membrane made of? describe
- what are 4 different types of proteins on the membrane?
A
- phospholipid bilayer! mostly phosphatidylethanolamine (glycerol + phosphate + ethanolamine + 2 FA)
- form a bilayer spontaneously bc of hydrophobic tail and hydrophyili head - protein channel, integral protein (embedded within membrane), peripheral protein, surface protein (type of peripheral protein
10
Q
what is the main difference btw cell membranes of bacteria, archaea and eukarya?
- why is it important ish?
A
- bacteria and eukarya –> ESTER bond btw glycerol and FA (C-O-C-R + C that attaches to FA also double bonded to another O)
VS archaea: ETHER bond btw glycerol and FA (C-O-C-R –> C not double bonded to O)
*archaea’s fatty acid chain is made of subunits of isoprene! - important to know bc allows to differentiate btw bacteria and archaea (if you discover a new species)
11
Q
describe the difference btw glycerol diether, diglycerol tetraether and crenarchaerol
- all of these can be found in which type of microorg? why?
A
GLYCEROL DIETHER
- normal glycerolphosphate + 2 phytanyls (FA chains made of isoprene units)
- makes a lipid bilayer!
DIGLYCEROL TETRAETHER
- 2 glycerol diether attached together –> glycerolphosphate + biphytanyl (super long) + glycerolphosphate
- makes one lipid monolayer! –> is stronger + resistant to high heat!
- made by archaea living in really hot temps (80-110°C)
CRENARCHAEROL
- like a diglycerol tetraether BUT rings are forms in the lipid layer, which makes it even stronger!
- in membrane of archaea! bc lipid chain is made of isoprenes!
12
Q
how is the cell membrane stabilized?
EUKARYA
BACTERIA
ARCHAEA
A
EUKARYA
- lipid bilayer is stabilized by sterol (polar head + RIGID planar steroid ring structure + nonpolar hydrocarbon tail)
- cholesterol for animal cells, ergosterol for fungi, stigmasterol for plant cells and some protozoans
BACTERIA
- sterols are almost always absent
- membrane stabilized by hopanoids –> same concept as sterols: hydrophobic substance + ring to hold structure together
ARCHAEA
- sterols are almost always absent
*RING = really strong, helps stabilize
13
Q
what is the size of
- plant/animal cell?
- polio virus
- protein
- mitochondria/bacteria
- flu virus
A
- plant/animal cell? 10 to 100 um, most are 100 um wide. some can be really big though
- polio virus: 50 nm ish
- protein: 5-10 nm
- mitochondria/bacteria: 1 um
- flu virus: 100 nm
14
Q
- size of cell depends on (A)
- (A) affects what?
- limit: ____-_____ in diameter
- what also affects (A)
- increase size will increase or decrease (A)
A
depends on surface volume ratio! –> affects exchange with outside (capacity to transport substrate across the cytoplasmic membrane)
- limit: 0.5-750 um in diameter
- SHAPE of cell also affects surface volume ratio –> sphere vs rod shape
- increase size of sphere will decrease surface/volume ratio –> bad bc can’t have enough transporters on surface to feed entire volume
15
Q
how do you go from DNA to protein? 3 steps with enzymes
A
- Replication of DNA by DNA polymerase
- transcription of bottom strand into RNA, by RNA polymerase
- translation into protein by ribosome, where codons are associated with correct aa
16
Q
storage of DNA: bacteria vs archaea vs eukarya
(5 info each)
A
BACTERIA AND ARCHAEA
- circular molecule, double stranded
- generally haploid (1 copy)
- packaged with proteins (H-NS and other histone-like proteins) –> aggregates to form the nucleoid, the chromosome
- DNA in cytoplasm, ribosomal RNA encoded on chromosome
- may also contain plasmids
EUKARYA
- linear molecules, double stranded
- generally diploid (2 copies)
- packaged with proteins (histones) to form chromatin fibers, the chromosome
- DNA in nucleus
- nucleolus: zone in nucleus that contains DNA that code for ribosomal DNA, ribosomal proteins, immature ribosome
17
Q
RIBOSOME
- composed of (2)
- translates ______ into __________ to form ________
PROKARYOTES:
- located where?
- prokaryote: ______ + _______ = ____ ribosome
- what sequence is used to look for phylogeny?
EUKARYOTE:
- located where?
- ______ + _______ = ____ ribosome
- what sequence is used to look for phylogeny?
A
- ribosomal RNA + proteins
- translates mRNA into aa chains to form proteins
PROKARYOTE (bacteria and archaea)
- free in cytoplasm OR attached to cytoplasmic membrane
- 30S + 50S = 70S ribosome
- 16S rRNA
EUKARYOTES:
- free in cytoplasm OR bound to ER
- 40S + 60S = 80S ribosome
- 18S rRNA
18
Q
what does the S in 30S or 70S ribosome stand for?
- describes what?
- proportional to what? (3)
- relationship is _______
A
Svedberg unit
- describes rate of sedimentation of a particles in an ultracentrifuge (50 000 rpm)
- proportional to size, shape and density of particle
- relationship is NOT linear
19
Q
which eukaryotes have a cell wall (3) vs absent in (2)
- cell wall forms a __________ –> function? (2)
- usually composed of __________ –> give examples
A
cell wall surrounds cells of plants, algae and fungi, BUT absent in animals and most protozoa
- forms a tough, rigid barrier that helps protect cell and gives its shape
- polysaccharides!
*plants, algae and some fungi: cellulose (polymer of glu)
*fungi: chitin (polymer of N-acetylglucosamine)
*also some cell walls made of galactose, mannose, etc. depends on species
20
Q
- DNA is stored as ____A_____ around __________ –> all condense into what?
- 2 types of (A)
A
- chromatin around histone proteins –> condense into chromosomes
1. euchromatin: loosely packed, actively TRANSCRIBED
2. heterochromatin: densely packed, low level of transcription
21
Q
- how many membranes does the nucleus have? –> what does that entail?
- where is mRNA translated? (2 ish)
A
- double membrane! 2 bilayer of phospholipids –> means that nucleotides, ATP, DNA/RNA polymerases, transcription factors have to be imported into the cells through pores
a) mRNA for cytoplasmic proteins: ribosome-mRNA complex stays free in cytoplasm
b) mRNA for membrane proteins, secreted proteins or vesicular proteins: ribosome-mRNA complex is directed to the ER
22
Q
ENDOPLASMIC RETICULUM
- ER is a system of ______________
- membrane is composed of what?
- rough ER: (2)
- smooth ER: (2)
A
- system of membranous channels
- composed of bilayer of phospholipid
- rough ER: studded with ribosomes, important for protein synthesis + modification + send them somewhere else
- smooth ER: NO ribosomes, lots of enzymes involved in synthesis of lipid (need compartment to keep them in = ER)
23
Q
explain 6 steps of an mRNA that will get translated in rough ER
A
- mRNA leaves nucleus and attaches of ribosome, protein synthesis begins
- signal recognition particle (SRP) binds to signal peptide (small piece of peptide that has been synthesized in (1) –> signals STOP, go to the ER
- SRP attaches to SRP receptor on ER; translocation channel opens, polypeptide enters ER
- signal peptidase removes the signal peptide and protein continues to be synthesized in ER
- ribosome subunits and mRNA break away
- protein folds into final shape in ER –> can also be modified (ie glycosylation and protein maturation in ER)
24
Q
which organelle is the “FedEx center of the cell?
- explain endocytosis VS exocytosis
A
Golgi apparatus!
EXOCYTOSIS:
- ie protein synthesized in ER –> vesicles containing protein originates from ER –> travels to Golgi apparatus –> gets a tag –> can go to mitochondria OR merge with secretory vesicle –> vesicle can merge with cell membrane –> secrete content extracellularly
ENDOCYTOSIS:
- vesicle fuses with membrane –> creates endocytic vesicle inside cell –> early endosome –> late endosome –> merges with lysosome (big bag of hydrolic enzymes –> can digest bacteria and spit out recycled material)
- endocytosis/phagocytosis
25
- what are endosome and vesicles? can do what?
- what are lysosomes?
- golgi body is what? function?
- how can proteins be secreted outside cells?
ENDOSOME AND VESICLES
- intracellular membrane-enclosed compartment
- can fuse with other membrane --> when 2 vesicles fuse together, their respective content is merged
LYSOSOMES:
- vesicles that contain hydrolytic enzymes required for degradation of materials brought in by phagocytosis and endocytosis via formation of phagosome or endocytic vesicles
GOLGI BODY:
- set of membrane compartments involved in further processing of proteins and their distribution
- proteins are packaged in vesicles and transported to where they are required
*proteins can be secreted outside the cells by secretory vesicles upon fusion with cytoplasmic membrane
26
MITOCHONDRIA
- outer membrane (2)
- inner membrane (a lot)
- matrix contains what (3)
- mitochondria can do what? + important for what?
*some _______ don't have mitochondria
OUTER MEMBRANE
- many porin proteins
- making membrane very permeable to small molecules
INNER MEMBRANE
- 75% proteins, 25% lipids
- transport proteins (regulated transport), enzymes, cytochromes, ATPases
- similar proteins are found in the membrane of bacteria and archaea
MATRIX
- enzymes (TCA cycle), circular DNA (have their own genome! can synthesize their own proteins ), ribosomes (70S, like prokaryotes!)
*can synthesize some of their own proteins, the remaining ones are imported from the cytoplasm of the cell (are encoded on its genome)
*important for respiration! --> produce more of ATP required by cells --> couples oxidation and reduction --> makes a proton motive force that allows phosphorylation of ADP + Pi to ATP
*protozoa
27
CHLOROPLAST
- present in what types of cells?
- OUTER MEMBRANE
- INNER MEMBRANE
- what are the names of 2 important structures?
- able to synthesize their own proteins?
- in phototrophic eukarya (plants, algae)
OUTER MEMBRANE
- porins, similar to mirochondria
INNER MEMBRANE
- transport proteins (regulated transport)
THYLAKOIDS:
- closed system of interconnecting sacks and tubules
- network of membranes --> where you find enzymes important for photosynthesis
STROMA (aka cytoplasm):
- circular DNA, 70S ribosomes (we thing it comes from bacteria), enzymes of Calvin cycle
* chloroplasts are able to synthesize some of their own proteins, the remaining ones are imported from cytoplasm of cell
28
THYLAKOIDS:
- contain what?
- similar proteins are found in what?
*what is the calvin cycle?
- contains enzymes and pigments that harvest light energy and membrane bound ATPases that use this energy to produce ATP
- similar proteins are found in many photosynthetic prokaryotes, usually in the cytoplasmic membrane
* fixation of carbon cycle! uses the ATP produced by light/proton motive force and + NADP+ produced from light
29
explain the acquisition of mitochondria and chloroplasts in eukarya
bacteria line --> has ancestor of chloroplast + ancestor of mitochondrion --> produce lots of energy
- archaea asks bacteria to live together --> evolve into eukarya --> 3rd domain appears (vs bacteria and archaea are the 2 basic ones)
30
what is the eukaryotic cytoskeleton? fct (2)
- found in prokaryotes?
- describe its components
- cytoplasm of eukaryotes contains a complex network of PROTEIN filaments that helps organize the cytoplasm and give cell its shape!
- similar proteins are found in several non-spherical prokaryotes
1. microtubules (green)
2. actin filament (red)
3. intermediate filament: keratin (important in skin cell), desmin, vimentin) --> just for structure, to hold everything together, ie hold nucleus in the middle of the cell
31
what are microtubules?
- serve as what?
- what are 2 important associated proteins?
- hollow structures composed of polymerized tubulin dimers (a-tubulin + b-tubulin --> polymerize/repeat themselves on several layers to form microtubules
- serve as 'highways" for the transport of organelles and vesicles around the cytoplasm (+ also provides resistance against squishing
- kinesin and dynein are 2 proteins that attach to vesicles or organelles and "walk" on microtubules transporting their cargo to where they are required (often from ER) + move organelles around the cell
32
- what is a centriole vs centrosome vs basal body?
- what are they made of? + function ish
CENTRIOLE:
- act as organizing centers for other microtubule arrays
- fct: organize microtubules
- 9 microtrubule triplets on the outside ish + 0 in the middle --> 200 nm diameter, 400 nm long
- eat set is composed of 1 complete microtubule + 2 partial microtubules = triplet
CENTROSOME:
- composed of 2 centrioles positioned at right angles to each other
- acts as a "flag" in the middle of the cell ish
- usually only 1 in a cell
BASAL BODY:
- centrioles that have migrated near the cytoplasmic membrane
- fct: organize construction of flagella or cilia + provides rigidity
- 9 + 0
BUT cilia and flagella of eukaryotes are:
- 9 sets of microtubule doublets (1 complete and 1 incomplete) + 2 complete microtubules in the middle
- covered by plasma membrane
33
what is the difference btw cilia and flagella?
- how do they move?
cilia = very short, thousands of them!
VS flagella = several length of the actual cell, usually only 1 or 2
- microtubules making up the cilia/flagella have dynein arms --> slide the doublets past each other, creating movement (ie grab another microtubule, and push itself up --> when all microtubules do it, creates mechanical work = movement!
34
SUMMARY of cytoskeleton of eukaryotes.
for each component:
- name
- structure
- subunit
- functions
ACTIN FILAMENTS (MICROFILAMENTS):
- strands in double helix
- actin
a) maintain cell shape by resisting tension (pull) (+ can change cell shape + involved in phagocytosis)
b) move cells via muscle contraction or cell crawling
c) divide animal cells in 2
d) move organelles and cytoplasm in plants, fungi and animals
INTERMEDIATE FILAMENTS:
- fibers wound into thicker cables
- keratin, or vimemtin or lamin, or others
a) maintain cell shape by resisting tension (pull)
b) anchor nucleus and some other organelles -->holds everything at their place
MICROTUBULES:
- hollow tube
- a and b-tubulin dimers
a) maintain cell shape by resisting compression (push)
b) move cells via flagella or cilia
c) move chromosomes during cell division
d) move organelles
e) provide tracks for intracellular transport
35
bacteria and archaea are both ____________
- differences with eukarya? (3)
- both prokaryotes
- no nucleus
- no compartments typically
- simpler organization
36
what are 6 shapes of bacteria and archaea?
- sphere (coccus)
- rod shaped (bacillus)
- bent rod (vibrio)
- short rod (coccobacillus) (crossover btw sphere and rod)
- wavy rod (spirillum)
- cork screw/tail of a pig (spirochete) --> Syphilis
37
how are bacteria and archaea arranged?
- ie coccus and rods
- single coccus (coccus)
- pair of 2 cocci (diplococcus)
- grouping of 4 cells arranged in a square (tetrad)
- chain of cocci (streptococcus)
- cluster of cocci (staphylococcus)
- single rod (bacillus)
- pair of rods (diplobacillus)
- chain of rods (streptobacillus)
- V- or L-shaped formation of rods (palisade)
38
- what gives the shape to a bacteria? = A
- 3 functions of A
- most species of bacteria can be classified according to what? --> name?
- do all bacteria have A?
cell wall!
1. allows bacteria to withstand intracellular osmotic pressure
2. is responsible for shape and rigidity of bacteria
3. plays an important role in cell division of bacteria
- can be classified into 2 groups according to the Gram's stain --> reflects fundamental differences in cell walls (and species)
- some species don't have a cell wall (ie mycoplasma, ie microbes that live in the human body)
39
what are the 4 steps of Gram staining?
- describe the color of Gram (+) vs Gram (-)
1. CRYSTAL VIOLET: primary stain added to the specimen smear
Gram (+): purple
Gram (-): purple
2. IODINE: mordant makes dye less soluble so it adheres to cell walls --> interacts with crystal violet to make it stick more
Gram (+): purple
Gram (-): purple
3. ALCOHOL: decolorizer washes away stain from gram (-) cell walls
Gram (+): purple (not recolorized by alcohol)
Gram (-): colorless
4. SAFRANIN: counterstain allows dye adherence to gram (-) cell wallls --> enhances ability to see gram (-) --> also stains gram (+) but purple is darker than pink/red
Gram (+): purple
Gram (-): red
40
compare and contrast cell walls of gram positive and gram negative bacteria
GRAM POSITIVE
- really thick peptidoglycan layer (where crystal violet and iodine can get stuck into) = cell wall
- peptidoglycan layer on top of usual cytoplasmic membrane
GRAM NEGATIVE
- cell wall = thin peptidoglycan layer + outer membrane (another bilayer)
- cell wall on top of usual cytoplasmic membrane
- space between 2 membranes = periplasm = a compartment
41
- peptidoglycan found in which domain of life?
- what is a peptidoglycan made up of?
- are there variants of peptidoglycan?
- what forms a subunit of peptidoglycan? what bond?
- what has never been found in archaea and eukarya (2)
- polymerization of sugar backbone: sequence?
- what does a lysozyme target?
- bacteria!
- peptidoglycan = polymer of peptidoglycan subunits (murein(?))
- many variants! (>100)
SUBUNIT:
- 2 sugars: N-acetylglucosamine (NAG) and N-Acetylmuramic acid (NAM) --> linked by b-1,4 glycosidic bond
- short peptide side chain containing unusual aa: D-aa (instead of L-aa found in proteins)
- NAM and diaminopimelic (DAP) acid have never been found in archaea and eukarya
- NAG-NAM-NAG-NAM-NAG... --> forms a long filament/strand
- link btw NAM and NAG (b-1,4 glycosidic bond) = target of lysozyme --> lysozyme secreted in tears, saliva and other body fluids to protect against bacterial pathogens! (by destroying cell wall of Gram (+) bacteria)
*doesn't affect gram (-) cell wall bc they have a second membrane
42
- peptidoglycan:
polymerisation of the sugar backbone provides what? only what? --> solution?
- what are the different linkages for gram positive vs negative
- provides rigidity to the structure only in 1 direction!
- another bond --> btw peptide chain of 2 adjacent peptidoglycan chains (side chains) provides rigidity in the other direction
GRAM (-) --> direct cross-linking --> side chains (ie DAP and d-Ala) are linked directly covalently
GRAM (+) --> interbridge cross-linking (also called transpeptidation) --> pentaglycine chain makes the link btw the chains --> why? makes more space between the ropes so that nutrient can pass through thick peptidoglycan more easily!
43
cell wall of gram-POSITIVE bacteria
- what % of wall is peptidoglycan?
- what are 2 components of the cell wall? decorated with (2), bound to what, how? function?
- how are wall-associated proteins attached to peptidoglycan?
- up to 90% of the wall is peptidoglycan!
- teichoic acid and lipoteichoic acid --> composed of glycerol-P (3C) or ribitol-P (5C) --> decorated with aa and sugars --> covalently bonded to peptidoglycan
- functions: Teichoic acid has a lot of phosphate groups = negative charge! (makes the gram (+) cell wall negative) + LTA attaches peptidoglycan to phospholipid of cell membrane
- wall-associated proteisn are attached covalently to the peptidoglycan by an enzyme called sortase!
44
cell wall of gram-NEGATIVE bacteria
- what % of wall is peptidoglycan?
- where is the peptidoglycan located? what does that space contain? sometimes called what?
- what else is the cell wall composed of? --> describe + 2 interesting characteristics ish
5-10% of cell wall
- located in periplasm! space delimited by cytoplasmic membrane and outer membrane --> contains high concentration of proteins involved in diverse functions, such as nutrient acquisition, extracellular enzymatic reactions, sensing, etc.
--> so dense that sometimes called "protein gel"
- outer membrane is an atypical lipid bilayer --> phospholipids in the inside layer, phospholipids AND lipopolysaccharide in the outside layer (LPS layer)
a) LPS helps protect the bacteria against a variety of substances, including antibiotics and against host defence system
- lipopolysaccharide --> a little extensions (lipid and sugar chain) --> keeps things away from surface + also charged negatively
b) outer membrane also contains outer membrane proteins (OMPs) such as porins, and lipoproteins which play a structural role
45
- what is LPS of gram (-) bacteria?
- 3 components --> describe each
lipopolysaccharide on the outer membrane of the cell wall
- LPS = a family of complex sugar polymers attached to a lipid moiety called lipid A
LIPID A:
- toxic to many animals as it induces inflammation (can lead to anaphylactic shock)
- is an endotoxin and plays a major role in the pathogenesis of gram(-) bacterial pathogens
- contains 6 lipid tails that are embedded in the membrane
- phosphate groups in the lipid A region and core region add negative charge to surface
CORE:
- made of polysaccs
- hydrophilic part (?)
O-ANTIGEN (on the big tail thing)
- o-specific polysaccharide, also known as O-antigen consists of repeating sequences of 2-4 monosaccharides
- diversity of O-antigens make it useful to identify different strains of one species of bacteria (ie E.coli O157:H7)
46
CELL WALLS OF ARCHAEA
- peptidoglycan in cell wall? outer membrane?
- consists mostly of what? (3)
- what is the main subunit ish?
- sensitive to lysozyme?
- peptidoglycan is ABSENT + usually no outer membrane
- cell walls of archae are diverse and may consist of proteins (usually), polysaccharides, and/or glycoproteins
- structure of pseudomurein (pseudopeptidoglycan) is similar to peptidoglycan --> contains N-acetyltalosaminuronic acid (NAT), instead of NAM and lacks D-aa
- b-1,3 linkage btw NAG and NAT --> insensitive to lysozyme!
47
- some species of archaea have a cell wall composed of repeating units of 2 or more sugars --> called what? vs what?
- great majority of cell walls of archaeal species consists of (2)
- these cell walls have a ___________ appearance when viewed by electron microscopy and are referred to as what (2 names)
- this can also be found in which domain of life? explain
- heteropolysaccharides (vs homopolysaccharides)
- proteins and/or glycoproteins
- crystalline appearance --> paracrystalline surface layer OR s-layers
- S-layer may also be found in some species of bacteria --> in this case, the S-layer forms an additional layer on top of peptidoglycan (gram-pos) OR on top of the outer membrane (gram-neg)
*viruses also have a shell that looks like the crystalline S-layer
48
bacterial and archaeal species may synthesize another layer known as (2 names), depending on its __________. --> does not confer what?
- composed mostly of (2) --> describe 2 types ish
- this may be ________ bound to which part of the cell wall?
- why is this part important?
- capsule OR slime layer, depending on its consistency --> does NOT confer significant strength to the cell
- composed of polysaccharides (vast majority) or proteins)
a) heteropolysaccharides (majority of bacteria)
b_ homopolysaccharides (some gram-neg)
- may be covalently bound to outer membrane OR to the peptidoglycan layer
- capsule is very important virulence determinant for capsulated bacterial pathogens --> the capsule protects against the host defence system! --> imparts chemical resistance!
*ie: protects gram-pos bacteria from lyzosomes!
49
REVIEW:
1) what are the 3 different filaments in cytoskeleton?
2) main component of flagellum in eukarya?
3) what is cell wall made of in bacteria?
4) target of lysozyme?
5) pseudopeptidoglycan susceptible to lysozyme?
1) actin filaments + intermediate filaments + microtubules
2) microtubules
3) peptidoglycan (gram positive has very thick + gram neg has outer membrane)
4) glycosidic bond btw NAM and NAG
5) no!
50
what are 2 types of surface appendages bacteria and archae can have?
- function? length?
- different types ish (for 1st one) + max speed?
- found primarily where (for 2nd one)
1) FLAGELLA
- used for locomotion/motility
- 15-20 um long (extend several times the size of the cell)
a) monotrichous (1 flagellum extending from 1 pole)
b) lophotrichous (many flagella originating from one end of cell, polar flagellation)
c) peritrichous (many flagella, all around the cell surface)
*max speed = 50 cell lengths/sec (vs cheetah max speed = 25 body lengths/sec)
2) FIMBRIAE
- primarily involved in attachment of microorganism to surfaces (other microorgs, nutrients, humans)
- form rigid, rod-like structures
- usually <= 4 um long
- found primarily on gram neg bacteria
51
describe the structure of bacteria flagellum (gram neg vs gram positive)
- 10 key words ish
- C ring (cytoplasm) and MS ring (membrane superficial) --> both embedded in cytoplasmic membrane + surrounded by MOT PROTEIN (anchored in peptidoglycan), which produce proton motive force
- P ring (peptidoglycan) --> embedded in peptidoglycan
- L ring (LPS): embedded in cell membrane (only in gram negative bacteria)
- all 4 rings = BASAL BODY
- there's a ROD in the middle of all the rings = seals the flagellum to the cell + allows to push ingredients out to the filament = can repair the flagellum!
- HOOK starts from the L ring --> becomes ish the FILAMENT which is made up of FLAGELLIN proteins (subunits that compose the filament)
52
how is the flagellum structure of bacteria powered? how does it move?
- powered by the proton motive force!
- the mot protein = electric motor ish --> make sure protons stay on 1 side --> makes the whole thing turn!
- the flagellum rotates which allows the bacteria to move around!
53
what is taxis? give examples
- give example of how a bacteria gets to where it wants
- taxis = directed movement toward or away from gradient of chemical or physical agents
- chemotaxis: chemicals, nutrients, antibiotics, etc.
- phototaxis: light (phototrophic organisms)
- aerotaxis: oxygen
- osmotaxis: ionic strength (salt concentration)
RUN and TUMBLE strategy!
- move forward (using flagellum)
- stop
- tumble on itself bc of random medium it's in
- move again
- stop
- if bacteria is moving toward right direction (using sensors), will just turn flagella longer to go where it wants
VS if not moving toward right direction --> will stop and hope to get tumbled into the right direction
54
1. what is the best studied fimbriae? --> describe its 2 fimbriaes
2. what is another name for fimbriae?
3. in contrast to flagella, fimbriae of gram negative bacteria grows how? assembly requires what?
4. how are the subunits assembled?
5. adhesion can be mediated by (2)
1. P fimbriae produced by uropathogenic E. coli (causes bladder infection
a) Type 1 pilus: can bind to anything that's charged
b) P pilus: specialized: can bind to bladder cells --> VIRULENCE FACTOR! gives bility to E.coli to infect and colonize bladder
2. pilus (pilli) and fimbriae
3. grow from the base! if it's cut, cannot repair it! have to rebuild it! --> bc sometimes, only the top subunit has the ability to bind, other subunits are just there for structure
- assembly requires chaperone and usher! chaperone = pore in outer membrane that shuttles proteins to the usher and puts it through the usher
4. subunits are assembled by strand exchange (like puzzle pieces) --> NOT covalently/chemically attached, like a lock and key
5. main subunits + specialized subunit at the tip (ie for P fimbriae)
55
compare fimbriae of gram positive vs gram negative bacteria
- anchored to what?
- composed of what?
- how are the subunits linked together?
- assembled how?
GRAM POSITIVE:
- anchored to peptidoglycan
- composed of pilin proteins
- covalently linked to one another
- assembled enzymatically by sortases
*in gram positives adhesion to surfaces is generally carried out by surface adhesins, consisting of only 1 protein. such adhesins mediate very close attachments
GRAM NEGATIVE:
- anchored in the outer membrane
- composed of pilin proteins
- NOT covalently bound to one another --> strand exchange!
- accessory proteins like chaperone and usher are needed@ encoded with the fimbriae pilin genes
56
- what is an endospore?
- is in what stage? and is easily dispersed by what?
- can remain in that stage for how long?
- best studied endospore?
- what do they look like from microscope?
spores that are inside bacteria --> highly differentiated cells that are extremely resistant to harsh environmental conditions: heat, chemicals, radiation, nutrient depletion, desiccation...
- (metabolically) dormant stage in life cycle --> easily dispersed by wind, water, animal digestive system, etc.
- can remain dormant for 100s of years (but probs a lot longer than that)
- clostridium species and bacillus species (gram positive)
- transparent to light! look white ish
57
what are the 5 layers of an endospore?
+ explain the functions of 4 specific "things"
1. exosporium: proteins (most outer layer)
2. coat: layers of the spore-specific proteins (keratin-like)
3. Outer membrane
4. cortex: peptidoglycan
5. core (cytoplasm): contains Ca2+, dipicolinic acid (DPA) and SASPs (small, acid soluble spore proteins)
- DPA and Ca2+ bind water and dehydrate the core! --> stops enzymatic reactions --> important for survival of endospore
- SASPs bind to DNA and help protect it against damage (ie UV light), like sunblock for DNA
- core contains proteins needed for germination
58
explain the steps for formation of the endospore. 6 steps
1. vegetative cycle = growing, fission into 2 daughter cells
2. when conditions start going bad (ie you boil the bacteria) --> starts an asymmetric cell division: 1/4 = forespore, 3/4 = mother cell
3. mother cell extends its membrane around the forespore = engulfment
4. forespore is now free in the mother cell and forms a forming coat + inner membrane + coat + cortex, etc. = late sporulation
5. mother cell lysis --> mother cell breaks, especially if continue boiling
6. endospore is now free and will germinate when conditions are back to normal
59
what are cell inclusions?
- may be enclosed by what?
- what do they store? 5 + explain ish
- in bacteria and archaea, energy reserves and building blocks are sometimes stored in granules or inclusions
- in some cases, cell inclusions can be enclosed by a single layer membrane (1 leaflet, no bilayer) --> phospholipid, protein, glycoprotein...
- lipid, sulfur, polyphosphate + some cell inclusions contain air = confer buoyancy
+ magnetosome contains magnetite (Fe3O4) and allows bacteria to respond to magnetic fields (magnetotaxis) --> use electric field to orient themself in space!
60
can bacteria be bigger than eukaryotes?
- what are some things specific to eukarya (7) vs to archaea/bacteria (7)? from the structure and function pptx
yes! giant bacteria!
EUKARYA:
- eukaryotic cell wall
- nucleus
- endoplasmic reticulum
- intracellular transport
- mitochondria
- chloroplast --> thylakoids
- eukaryotic cytoskeleton: microtubules, centrioles, basal bodies, cilia, flagella
BACTERIA AND ARCHAEA:
- cell wall
- bacteria: gram stain: peptidoglycan + LPS
- archaea: pseudopeptidoglycan, S-layer
- capsule and slime layers
- surface appendages: flagella and fimbriae
- endospore
- cell inclusions
