2. Structure and function Flashcards

Question

- what are endosome and vesicles? can do what? - what are lysosomes? - golgi body is what? function? - how can proteins be secreted outside cells?

Answer 1

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

Answer 2

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

Answer 3

- 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

Answer 4

- 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

Answer 5

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)

Answer 6

- 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

Answer 7

- 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

Answer 8

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

Answer 9

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!

Answer 10

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

Answer 11

- both prokaryotes - no nucleus - no compartments typically - simpler organization

Answer 12

- 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

Answer 13

- 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)

Answer 14

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)

Answer 15

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

Answer 16

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

Answer 17

- 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

Answer 18

- 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!

Answer 19

- 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!

Answer 20

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

Answer 21

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)

Answer 22

- 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!

Answer 23

- 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

Answer 24

- 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!

Answer 25

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!

Answer 26

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

Answer 27

- 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)

Answer 28

- 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!

Answer 29

- 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

Answer 30

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)

Answer 31

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

Answer 32

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

Answer 33

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

Answer 34

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

Answer 35

- 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!

Answer 36

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

2. Structure and function Flashcards

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