Ch. 3 - Cell Structure & Function in Bacteria & Archae (Ch. 4 -- 12 ed.) Flashcards
1
Q
Central Dogma of Molecular Bio
(pp. 176, 252)
A
- Genetic material in the cell specifies the organization of the cell & its activity
- Molecular processes (underlying genetic info flow) can be dividied into 3 stages:
- Replication - DNA is duplicated, producing two double helices
- Transcription - DNA participates in protein synthesis through an RNA intermediate (mRNA)
- -> some genes contain info for other types of RNA: tRNA & rRNA
3. Translation - sequence of amino acids in a polypeptide (making up a protein) is determined by the specific sequence of bases in mRNA
–> In Eukaryotes…each gene transcribed to give a single mRNA
–> in Prokaryotes…a signle mRNA may carry genetic info from several genes
2
Q
Mimi Virus exception(s)?
A
- Viruses contain only a single form of nucleic acid – either DNA or RNA
–> Mimi virus contains both RNA & DNA
3
Q
Major Cell Morphologies
A
–> several morphologies are known among prokaryotes…
- Coccus – spherical or ovoid
- Bacillus (rod) – cylindrical shape
- Spirilla – some rods twist into spiral shapes
–> several groups possess unusual shapes…
- Spirochets – tightly coiled shape
- Appendaged – possess extensions of their cells (hypha/stalks)
- Filamentous bacteria – long, thin cells/chains
- Vibrio – half-moon shaped
**Cell morphology is easily recognized…but generally a poor predictor of a cell’s other properties**
4
Q
Describe Cell Size of Prokaryotes
- Esherichia coli?
- Thiomargarita namibiensis?
- Mycoplasma pneumoniae
A
- Prokaryotes vary in size from ~ 0.2 µm to ~ >700 µm (in diameter)
- -> 1 µm (micrometers) = 10-6 m (meters)
- E. coli = 2 µm
- -> considered base volume for prokaryotic cells
- -> E. coli vol. = 2 µm3 –> (EC vol. = 1)
- T. namibiensis = 750 µm
- -> T. namibiensis vol. = 200,000,000 µm3 –> (EC vol. = 108
- M. pneumonia = 0.2 µm
- -> M. pneuonmia vol. = 0.005 µm –> (EC vol = 2.5 x 10-3)
5
Q
Significance of Small size of Prokaryotes
A
- prokaryotic cells generally very small cells compared to eukaryotes
- -> very large…not common
- rate at which nutrients/waste products transport in/out of cell is generally **inversely proportional to cell size**
- -> higher S/V (surface are/volume) ratio of smaller cells supports greater nutreint exchange per unit of cell volume…vica versa…
- -> cell’s growth rate depends (among other important things) on the rate of nutrient exchange
**S/V = 3/r** (for spherical coccus..)
⇒ larger the cell…smaller the S/V ratio –> results in a lesser efficient exchange with environment
6
Q
Structure of Viruses
A
Viruses come in numerous sizes & shapes…most smaller than prokaryotic cellsg
- Acellular…thus “nonliving”
- -> rely on host cells to provide E & materials needed for replicationg their genomes & synthesizing their proteins…**Obligate intracellular parasites**
- Nucleic acids – contain either DNA or RNA.. (NOT both)
- -> (exception)…Mimi Virus contains both DNA & RNA
- Capsids – protein shell which surrounds nucelic acid of virion
- -> made up of Capsomers (structural subunits)
- -> Nucelocapsid – complete complex of nucelic acid & protein packaged in virion
7
Q
Viriods
A
- infectious RNA molecules that differ from viruses…lack capsids (protein coat)
- consist of single-stranded (covalently-closed) circular RNA that forms a seemingly double-stranded structure by intra-strand base pairing
- -> makes it stable to exist outide of host cell… (NOT an obligate intracellular parasite)
- -> enters through wound in plant cells… (does not use a receptor to enter host like viruses)
- **interferes with regulatory RNA in plants**…
- -> viriods possess no protein-encoding genes…basically totally dependent on host function (for replication)
- -> viroid replicated in host cell nucleus or chloroplast by plant RNA polymerases
- NO animal diseases known
8
Q
Prions
A
- thought to be small replicating polypeptides
- -> contain neither RNA or DNA
- Mechanism of Prion misfolding:
- -> neuronal cells produce normal form of prion protein (PrPC)
- -> Pathogenic form (PrPSc) catalyzes refolding of normal prions into abnormal form… (PrPC into PrPSc)
- PrPSc is protease resistant & insoluble…aggregates in host neural cells (brain cells)
- infectious in animals only
- -> Mad Cow Disease in cattle
- -> Creutzfeldt-Jakob disease (CJD) in humans
9
Q
General structure of Phospholipid Bilayer
A
- main constituent of cytoplasmic membrane
- -> separates cytoplasm from environment
- -> highly selective permeability barrier
- -> if broken…integrity of cell is destroyed
- possess both hydrophobic (fatty acids) & hydrophilic (glycerol-phosphate) components
- -> hydrocarbon chains (of fatty acid) points inward
- -> glycerol-phosphates point outward toward environment & cytoplasm
- 6-8 nm wide
- viewed from electron microscope…appears as 2 light-colored lines separated by a darker area
10
Q
Describe in-depthly composition of Phospholipids
–> chemical make-up…
A
- consists of hydrophobic fatty acids (hydrocarbon chains) *esterified* to glycerol
- -> **removal of H20 between alcohol group (from glycerol) & caroxyl group (from 2 fatty acids OR 1 phosphoric acid)**
11
Q
Cytoplasmic membrane Proteins
–> 2 types…
A
- Peripheal Proteins (extrinsic proteins)
- not embedded…but still associated with membrane surface
- some easily removed from changes in environment (pH, ionic strenght, etc…)
- typically on surface of membrane
- some may be bound to integral proteins…important cellular processes (energy metabolism, transport, etc…)
- -> some are *Lipoproteins*… proteins containing lipid tail that can anchor integral proteins
- Integral Proteins (intrinsic proteins)
- firmly embedded in membrane
- many span entire membrane but not all…possessing external & internal surfaces
- -> must be *ampipathic* (both hydrophilic & hydrophobic regions)…hydrophobic inside membrabe & hydrophilic internal/external surfaces of membrane
**Cytoplasmic proteins are arranged in clusters** (NOT being distributed evenly)
- -> allows grouping of proteins that interact or that have similar function
- -> Lipid bilayer varies in thickness (from 6 - 8 nm) to accommodate various patches of proteins
12
Q
Cytoplasmic Membrane Function
A
- Permeability Barrier
- prevents leakage (which would distruct integrity of cell)
- functions as a gateway for transport of nutrients into and out of cell
- Protein Anchor
- site of many proteins involveed in transport, bioenergetics, signaling, & chemotaxis - Energy Conservation
- site of generation & use of proton motive force
- -> *Proton Motor Force* – membrance possesses a charge separation (in which protons & hydroxyl ions are separate across surface)… results in form of energy
- -> responsible for driving many energy-requiring functions in cell
- -> includes some forms of transport, motility, and biosynthesis of ATP
13
Q
Proton Motive Force
A
- factor that gives cytoplasmic membrane ability to function as major site of E conservation in cell
- **membrane possess an energetically charged form in which protons (H+) are separated from hydroxyl ions (OH-) across its surface**
- -> charge separation is a form of E…analogous to potential E
- -> responsible for driving many E-requiring functions in cell…some forms of transport, motility, biosynthesis of ATP
- bc of charged membrane…charged molecules (even as small as a proton H+) canNOT passivle transport across membrane
14
Q
Sterols
A
- Eukaryotes possess **Sterols** in their membranes (while almost all prokaryotes do NOT)
- -> (exceptions… 2 prokaryotes that do possess Sterols – Mycoplasmas)
- -> Mycoplasmas lack cell walls…require Sterols to stabilize their membrane
- Steroles make up anywhere from 5% - 25% of total lipids in eukaryotic membranes
- Sterols are rigid planar molecules & the association of these with the membrane serves to *stabilize* its structure making it less flexible
- -> Fatty Acids are more flexible
15
Q
Hopanoids
A
- similar to Sterols…rigid, planar molecules which strengthen & stabilize membrane making it less flexible
- ***present in many Bacteria***
- -> NOT present in Archaea
- widely distributed example = *Diplotene (C30)*
16
Q
Achaeal Membranes
A
- Archaea lipids are chemically unique
- -> possess ***Ether*** linkages between L-glycerol & their hydrophobic side chains…
- -> …Bacteria & Eukarya possess *Ester* linkages between D-glycerol & fatty acid hydrocarbon chains
- Archaea lipids lack fatty acids…
- -> … possess side chains of repeating units of parent 5-carbon hydrocarbon **Isoprene** [(c) of image @ bottom]
***it was 16S rRNA sequence differences that led Woese to discover Archaea as a new domain…distinct from Bacteria & Eukarya***
17
Q
Major Lipids of Archaea
A
(both still possess repeating units of Isoprene side chains)
- ***Glycerol diethers***
- -> possess 20-C side chains… (4 linked Isoprene units)
- -> …*Phytanyl* – 20-C side chains
- ***Diglycerol Tetraethers***
- -> possess 40-C side chains… (8 linked Isoprene units)
- -> …*Biphytanyl* – 40-C side chains
- -> 2 phytanyl from each glycerol molecule are covalently bonded together – Tetraether actually called Di-biphytanyl diglycerol tetraether
- (in Tetraether lipids)…
- -> within a membrane, this structure yields a lipid ***monolayer***
- Lipid Monolayers are resistant to peeling apart
- -> monolayer membranes widespread among hyperthermophilic Archaea, prokaryotes…prevents cell lysis
18
Q
Necessary Properties of Transport Proteins
A
- transport systems demonstrate **Saturation Effect**
- -> carrier proteins are saturable sometime even at low [solute]
- -> rate of uptake becomes maximal @ substrate saturation & addition of more solute does not increase the rate
- has high specificity
- -> many carrier protons react only with a single molecule
- -> others show affinities for closely related class of molecules (such as sugars; amino acids)
- biosynthesis of transport proteins is typically regulated by cell
- -> function of both nutrients present in environment & their concentrations
- -> particular nutrient may need to be transported by one transporter when at high [given nutrient]….and by a different (higher-affinity) transporter when at low [given nutrient]
19
Q
Rate of Solute Entry
A
**Y axis : Si
**X axis: Time
- Initial velocities of transport: /\Si/ /\T
- velocities meased when Si is initially 0 & S0 is varied & rate is measured @ early times
- each line represents a different initial [solute] on outside, S0
- eventually *max velocity* is achieved
- -> arrow line would be same for S4, S5, S6, etc…
- -> Vmax of transport reached
20
Q
Types of Passive Transport
A
**do not utilize source of E**
–> solute travels down conc. gradient…
…from [high] to [low]
- **Net transport internally when [S]o > [S]i**
–> if [S]o = [S]i then v = 0
- Simple Diffusion
- non-saturable - Facilitated Diffusion
- saturation @ high [solute]
- -> carrier proteins possess specificity for solute
21
Q
Types of Active Transport
A
**use E to accumulate solute against conc. gradient**
–> transports from [low] to [high]
- Simple Active
- utilize Ion gradients/*Proton Motice Force*
- consists of only a membrane-spanning integral protein
- ATP-binding Cassette (ABC) System
- E from ATP
- consists of 3 components: 1) substrate-binding protein; 2) membrane-integrated transport; 3) ATP-hydrolyzing protein
–> 2 ATP → 2 ADP + 2 Pi
- Group Translocation
- E from chemical modification of transported substance (phosphorylation) driven by Phosphoenopyruvate
- involved series of proteins in transport event
22
Q
Membrane Spanning Proteins & their structural similarities which correspond to their ability to act as Transporter membranes
–> 3 classes of transport events?
A
- contain 12 alpha-helix domains that weave back & forth forming channels which solutes enter cell
–> transport event involves protein *conformational change* upon solute binding…
…this shuttles solute across membrane
3 clases of transport events:
1) Uniporter
- proteins that transport a molecule unidirectionally across membrane
2) Antiporter
- proteins that transport a molecules across membrane while simultaneously transporting a second molecule in *opposite* direction
3) Symporter
- proteins that transpot a molecule across membrane while simultaneously transporting a second molecule in *same* direction
- -> frequents a proton (H+)
- -> function as *cotransporters*
23
Q
Phosphotransferase System
A
- best studied model of *group translocation*
–> type of active transport – requires E…
…energy from PEP (Phosphoenol-pyruvate)
–> results in phophorylation (chemically modification) of substance being transported - **Phosphotransferase Sys. transports the sugars glucose, mannose, & fructose in E. coli**
- consists of a family of proteins…5 of which are necessary for given sugar
- (before transport of sugar) these proteins are alternately phosphoylated & then dephosphorylated in cascading fashion … until the actual transporter (Enzyme IIC) phosphorylates the sugar
- Enz I; HPr; Enz IIa are all cytoplasmic proteins
- Enz IIb lies on the inner surface & Enz IIc is an integral protein
- Enz I & HPr are non-specific components
- all Enz II proteins are specific components…
- -> specific Enz II exists for each sugar (glucose, fructose, & mannose)
***phosphorylation of Glucose to Glucose-6-P is 1st step in its intracellular metabolism – Glycolysis***
24
Q
The ABC System
A
ATP-binding Cassette
–> necessary for uptake of organic compounds (sugars, amino acids) & inorganic compounds (sulfate & phosphate) & trace metals
**Gram- (-) bacteria possess Periplasmic region**
- -> Periplasm – lies between cytoplasm & peptidoglycan
- -> periplasm contains many different periplasmic-binding proteins
- Gram- (+) bacteria also have ABC systems
- -> substrate-binding protein anchored to external surface of cytoplasm
ABC System:
- ATP hydrolyzing protein (Kinase) provides E
- 3 components
1) Periplasmic (substrate) - binding protein
–> located in periplasm
–> typically high substrate affinity
2) membrane-spanning transporter protein
3) ATP-hydrolyzing protein (Kinase)
2 ATP → 2 ADP + Pi
25
Q
Protein Transport
A
- cell to function properly…proteins transported through cytoplasmic membrane or inserted into membrane
- -> possible by **Translocases**
- many bacterial enzymes function as exoenzymes
- Preproteins – presecretory proteins which synthesize transported proteins
- -> preproteins possess a signal peptide at amino terminus…recognized by Sec System
- -> Chaperon – proteins that bind to signal peptides & delay protein folding (keeping it in necessary conformation for transport)
- -> Signal Peptidase – remove signal peptide & protein folds into shape
- key example – *Sec (secretory) System*
- -> both exports/inserts into membrane - consists of 7 proteins:
1) Sec Y, E, G – transmembrane transporter proteins
2) Sec A – ATP hydrolyzing enzyme (energy)
3) Sec B – prevents folding of protein in cytoplasm
4) Sec D, F – assists in translocation
- -> also consumes E from Proton Motive Force
26
Q
Function of Cell Wall of Bacteria
A
*bc of activities of transport systems…cytoplasm of bacterial cells maintains a high [dissolved solutes]*
- protects cell from Osmotic Pressure & prevents Cell Lysis
- -> bacteria tend to live in environments typically hypotonic to cell…thus H20 tends to move into cell
- -> this causes significant Osmotic Pressure…would cause cell lysis if it were not for rigid cell wall
- confers shape & regidity to cell
27
Q
Gram + vs Gram - Bacteria cell walls
A
- **Peptidoglycan is rigid layer primarily responsible for strength of cell wall**
- Gram + :
- -> 1 thicker layer of peptidoglycan
- -> Gram stain test results in Purple stained cells
- -> B. subtilis
- -> S. aureus
- Gram - :
- -> 2 layers – thin peptidoglycan + LPS
- -> Gram stain test results in Pink stained cells
- -> E. coli
28
Q
Composition of Peptidoglycan
A
- rigid layer or sheet
- -> thick in Gram +
- -> thin in Gram -
- composed of 2 sugar derivatives: N-acetylglucosamine (G) & N-acetylmuramic acid (M)
- -> always connected in Beta-1,4 glycosidic bond
- also composed of small group of amino acids: L-alanine & D-alanine, D-glutamic acid; either Lysine (gram +) or Diaminopimelic acid (DAP) (gram -)
29
Q
DAP vs Lysine
A
- 2 of numerous amino acids found in peptidoglycan cell wall of bacteria
- identical in chemical structure besides terminal end
- Gm (-):
- -> possess DAP (Diaminopimelic Acid)
- -> E. coli
- -> - COOH
- Gm (+):
- -> possess Lysine
- -> B. subtilis
- -> S. aureus
- -> - H
30
Q
Peptidoglycan variations: Cross-links & interbridge connections
A
**Glycan backbone portion constant among all species of Bacteria**
- -> G-M-G-M (N-acetylglucosamine & N-acetylmuramic acid)
- -> beta 1,4 Glycosidic bond
- Tetrapeptide variation only in 1 amino acid in ***position 3*** – DAP/Lysine
- Gm (-):
- -> amino group (- NH2) of DAP cross-linked to carboxy group (- COOH) of terminal D-alanine via **peptide bond**
- -> NO interbridge
- Gm (+):
- -> cross-linkage occurs via **peptide interbridge**
- -> kinds & numbers of amino acids in interbridge vary from organism to organism
- -> interbridge in S. aurerus…consists of Glycine pentapeptide bridge
31
Q
Peptidoglycan Sheet
A
- Glycosidic bonds confer strength in X direction
- Peptide bonds confer strength in Y direction
32
Q
Diversity of Peptidoglycan
–> Defining characteristics…?
A
- only present in species of Bacteria
- sugar N-acetylmuramic acid (M) & amino acid Diaminopimelic acid (DAP) never found in cell walls of Archaea or Eukarya
- most Gm (+) possess Lysine instead of DAP
- -> 3rd molecule distal from M
- (unusual feature) presence of 2 amino acids that are D-configuration (D-alanine & D-glutamic acid)
- greatest diversity in peptide crosslinks & interbridge
- -> Gm (+) – Lysine – cross-linkage @ peptide interbridge bond (Lysine & varying amino acid bridge of adjacent glycan chain)
- -> Gm (-) – DAP – cross-linkage @ peptide bonds (DAP & D-alanine of adjacent glycan chain)
- Gm (+) possess more cross-links
- Gm (-) possess cross-links that are “longer”
33
Q
Teichoic Acids
A
- acid substances embedded in cell wall
- -> of Gm (+) Bacteria
- bc of (-) charge of Teichoic acids…partially responsible for (-) charge on Gm (+) cell surface as whole
- encompasses all cell wall, cytoplasmic membrane, & capsular polymers containing *polyalcohols*
- -> Polyalcohols – glycerophosphate; ribitol phosphate residues
- (in wall) covalently bound to N-acetylmuramic acid via **Phosphate Esters**
- -> usually possess D-alanine & other sugars attached
- **Lipoteichoic acids** – teichoic acids covalently linked to membrane lipids (Lipoproteins)
34
Q
Lysozyme
A
- Peptodoglycan can be destroyed by certain agents
- -> causes weakening of cell & possibly eventual cell lysis
- -> such as **Lysozyme**
- -> Lysozyme – protein that breaks the B-1,4-glycosidic bond between N-acetlymuramic acid & N-acetyl glucosamine
- -> Lysozyme function as major line of defense against bacterial infections via this mechanism
35
Q
Protoplasts
A
- a Gm (+) bacterium that has lost its cell wall
- -> did not under cell lyses
- -> destruction of peptidoglycan caused from agents such as Lysozyme
- Lyses occurs….
…in dilute solution bc cell wall is structurally very weak - Lyses does NOT occur…
…in solutation containing an **isotonic** concentration of a solute (such as Sucrose)
…H20 does NOT enter cell
⇒ ***Protoplasts only possess cytoplasmic membrane & internal constituents***
–> devoid of cell wall; no residual wall left
36
Q
Spheroplasts
A
- Gm (-) bacteria produce Spheroplasts when treated with Lysozyme
- (similar to protoplasts)…but possess residual wall attached
37
Q
Examples of Cells that lack Cell Walls
A
- Mycoplasmas
- -> group of pathogenic bacteria that cause variety of infectious diseases in humans & other animals
- -> like protoplasts & live in osmotically protected environment
- -> Sterols add strength to membrane
- -> …Lysozyme found in animal secreations…
- Thermoplasmas
- -> species of Archaea that naturally lack cell wall
- -> unusually tough cytoplasmic membranes
38
Q
Pseudomurein
A
- found in some Archaea cell wall
- -> Methanogenic Archaea
- constructed of a polysaccharide very similar to Peptidoglycan
- backbone composed of alternating repeats of N-AcGlu & N-acetyltalosaminuronic acid (T)
- -> Glycosidic bonds are B-1,3 (instead B-1,4)
- -> Lysozyme-insensitive
- possess Lysine as 3rd position on Glycan Chain
- possess only L steroisomer
- some archae have S layers
39
Q
Penicillin
A
- type of Beta-lactam ring antibiotic
- potent inhibitors of cell wall synthesis
- -> disrupts formation of cross-links
- -> bind to Transpeptidase enzymes
- Archae naturally resistant to Penicillin (& Lysozyme)
- Bacteria affected by both Penicillin & Lysozyme
40
Q
S layer
A
- most common cell wall type among Archaea
- Paracrystalline surface layer (or S layer)
- -> showed ordered appearance under microscope
- -> typically hexagonal symmetry
- consists of protein or glycoprotein
- provides some protection from osmotic lysis
- -> many organisms possess both S layer & peptidoglycan – (S layer being the outermost)
- selective sieve
- -> not alloweing large molecules in (such as viruses)
- may retain proteins near surface
41
Q
Lipopolysaccharide layer (LPS)
A
- Gm (-) bacteria possess outer LPS in addition to peptidoglycan
- contains polysaccharides & phospholipids…
- -> … linked in outer membrane to form lipopolysaccharide structures
42
Q
Structure of LPS
A
- 3 components:
1) O-specific polysaccharides
- often branched
- most external facing component
2) Core polysaccharides
3) Lipid portion (Lipid A)
- most internal portion of LPS
- is endotoxic (toxicity to animals)
- embedded in phospholipid portion
- -> lipoproteins present on inner side of LPS anchor outer membrane to peptidoglycan
- considered lipid bilayer but distinct from cytoplasmic membrane
43
Q
Endotoxin
A
- LPS layer [Gm (-)] bacteria commonly toxic to animals
- toxic properties associated with Lipid A
- -> Innermost portion of LPS
- produce fever, decrease B.P., activation of inflammation, coagulation of blood
presence in blood can lead to **septicemia**
44
Q
LPS Permeability & Porins
A
- LPS not permeable to large molecules (proteins)
- -> major function – prevent proteins from diffusing - O-specific polysaccharides prevent hydrophobic molecules from diffusing pass LPS
- -> hydrophobic antibiotics not effective to Gm (-)
- Lipid A phspholipid layer prevent hydrophilic small molecules from diffusing pass LPS
- **Porins** – proteins present in LPS
- -> function as channels for entrance/exit of hydrophilic low-molecular-weight substances
- -> H20 filled channels
- -> several different porins exist…both specific & nonspecific
- consists of 3 identical subunits
45
Q
Capsules vs. Slime Layers
A
both may be thick/think; rigid/flexible depending on chemical makeup & hydration
- Capsules
- material organized in tight matrix (like an envelope around cell)
- exclused small particles – such as india ink
- Slime layers
- material more easily deformed; organized in loose matrix
- will not exclude particles; more difficult to see
46
Q
Functions of Capsules
A
- attachment of microbes to solid surfaces
- -> pathogens typically first bind to surface components on human tissues
- -> nonpathogenic often bind to surfaces in nature – forming Biofilm ( – thick layer of cells)
- encapsulated pathogenic bacteria more difficult for phagocytic cells to engulf & destroy
- polysaccharide layers bind water & may make cells resistant to desiccation (drying)
47
Q
Fimbriae & Pili
A
- both filamentous structures composed of protein that extend from surface of cell
- -> not typically involved in motility even though similar to flagella
- allow cells to stick to surfaces
- -> including animal tissue
- Fimbriae are considerably shorter than flagella & are more numerous
- Pili are similar to fimbriae but typically longer & only 1 or a few present on cell surface
48
Q
Functions of Pili
A
pili often receptors for certain types of viruses…
–> can best be seen under electron microscope when they have become virus-coated pilus
- *Congugation* – facilitation of genetic transfer between prokaryotic cells
- -> F+ (donar) x F- (recipient) ⇒ F- becomes F+
- -> F factor (Plamid) transferred while replicated
- *Adhesion of pathogens* to specific host tissue
- *Cell Twitching* – unusual form of cell motility
