Chapter 2-3-4: Prokaryotic Cell Structure & Function Flashcards
(154 cards)
1
Q
Microscope
A
set of 2 or more lenses
2
Q
Parts Necessary to Have Functional Microscope
A
- light source
- objective lenses
- coarse & fine adjustment knobs
- ocular lenses
- diaphragm
3
Q
Microscopy Concepts
A
- Magnification
- Resolution
- Illumination
4
Q
- Magnification (Job of the Lenses)
A
increase in the apparent size of the specimen
- increases size of image (not object)
calculated by multiplying magnification factor of lenses
= objective x ocular
5
Q
- Resolution
A
the minimum distance that two objects can be separated from one another, and still be recognized as distinct objects rather than 1 larger “fuzzy” object
- minimum distance between 2 objects where they still are seen as 2 different objects
6
Q
- Resolution (Increasing Resolution)
A
- oil: higher refractive index than air (allows light to stay and be collected into objective lens)
- decreasing illumination wavelength (smaller the wavelength, better the detail ex. slide 10)
- focusing illumination light (condenser) helps focus light
7
Q
Resolution VS Magnification
A
Magnification: refers to the enlargement of the image
Resolution: refers to the ability to distinguish two objects located very close as being separated entities
(higher #= better the resolution)
8
Q
- Illumination: Brightfield
A
method of lighting the specimen from opposite the objective
- specimen appears dark against a light background
- common method of lighting
- specimen interferes with light coming through
9
Q
- Illumination: Darkfield
A
- illumination of the specimen without projecting light directly into the objective
- used to examine specimens which cannot be distinguished from the background
- unstained; living
- accomplished by specialized microscopic lighting techniques
10
Q
Preparation & Staining of Specimens (Purpose & Process)
A
Purpose:
- increased visibility
- accentuates specific morphological features (enhancing)
- preserves specimens
Process:
- fixation
- staining
- visualization
11
Q
Fixation
A
preservation of internal & external structures
- organism is killed and firmly attached to microscope slide
12
Q
Methods: Heat & Chemical Fixing
A
Heat Fixing:
- good for maintaining external structures
- preserves overall morphology (not internal structures)
Chemical Fixing:
- protects fine cellular substructure and morphology of larger, more delicate organisms
- well preserved internal structures
13
Q
Staining: 1. Dyes & Simple Staining- Dyes
A
Dyes: makes structures more visible & increase contrast
- cell structures more visible
- increasing contrast
- common features
- chromophore groups (color)
- ability to bind cells
- types
- basic + charged (bind to - charged cells ex DNA)
- acidic - charged
14
Q
Staining: 1. Dyes & Simple Staining- Simple Staining
A
- single agent
- frequent used basic dyes
- e.g crystal violet; methylene blue
15
Q
Staining: 2 Differential Stains
A
divides microorganisms into groups based on their staining properties
Examples
- gram stain (most widely used- allows differentiation between gram + & gram - bacteria)
- acid-fast stain
- staining of specific structures
16
Q
Gram Staining
A
- Christian Gram (1884)
- most widely used
- two groups
- Gm+, Gm-
- differences in cell wall structure
17
Q
Mordant
A
compounds that like to stick
18
Q
Example of Getting Info From Name: Staphylococcus
A
staphylo- grape (bacteria sticks together)
coccus- sphere (sphere shaped)
19
Q
Acid-Fast Staining
A
- stains bacteria that is hard to stain
- stains Mycobacterium- cannot be stained by Gram staining (cell wall made of thick lipids)
- e.g. M. tuberculosis; M. leprae
- staining characteristics: high lipid content in cell walls
20
Q
Negative Staining
A
- visualize capsules
- colorless against a stained background
- capsules are sensitive (do not use heat fixation) instead air-fix specimen
- structure you’re trying to visualize stays colorless
21
Q
Spore Staining
A
- double staining technique
- bacterial endospore (resistant) vs. vegetative cell (cell growing actively)
22
Q
Flagellar Staining
A
mordant to increase thickness of flagella
23
Q
Phase-Contrast Light Microscopy
A
- living cells (not fixed)
- no stain
- light reflects from specimen
24
Q
Electron Microscopy
A
- transmission (cut specimen in very thin slices) see details IN specimen
- scanning (use electrons to scan surface of the specimen) see details ON specimen
25
Overview of Prokaryotic Cell Structure
- a wide variety of sizes, shapes, and cellular aggregation patterns
- simpler than eukaryotic cell structure
- unique structures not observed in eukaryotes
26
Cocci (s., coccus)- spheres
- diplococci (s., diplococcus)- pairs
- streptococci- chains
- staphylococci- grape-like clusters
- tetrads- 4 cocci in a square
- sarcinae- cubic configuration of 8 cocci
27
Bacilli (s.,bacillus)- rods
- coccobacilli- very short rods
28
Overview of Prokaryotic Cell Structure: Vibrio
"comma" shaped
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Overview of Prokaryotic Cell Structure: Spirilla
s.,spirillum- rigid helices
30
Overview of Prokaryotic Cell Structure: Spirochetes
flexible helices
31
Can you differentiate between spirilla and spirochetes?
No, you can't differentiate them unless they're moving
32
Overview of Prokaryotic Cell Structure: Filamentous
form hyphae
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Overview of Prokaryotic Cell Structure: Mycelium
branched hyphae
34
Overview of Prokaryotic Cell Structure: Pleomorphic
bacteria without a single characteristic shape (form)
35
Plasma Membrane
selectively permeable barrier, mechanical boundary of cell, nutrient and waste transport, location of many metabolic processes (respiration, photosynthesis), detection of environmental cues for chemotaxis
36
Gas Vacuole
an inclusion that provides buoyancy for floating in aquatic environments
37
Ribosomes
protein synthesis
38
Inclusions
storage of carbon, phosphate, and other substances; site of chemical reactions (microcompartments); movement
39
Nucleoid
localization of genetic material (DNA)
40
Periplasmic Space
in typical Gram-negative bacteria, contains hydrolytic enzymes and binding proteins for nutrient processing and uptake; in typical Gram-positive bacteria, may be smaller or absent
41
Cell Wall
protection from osmotic stress, helps maintain cell shape
42
Capsules and Slime Layers
resistance to phagocytosis, adherence to surfaces
43
Fimbriae and Pilli
attachment to surfaces, bacterial conjugation and transformation, twitching
44
Flagella
swimming and swarming motility
45
Endospore
survival under harsh environmental conditions
46
Bacterial Cell Envelope
contains plasma membrane and surrounding layers
47
Bacterial Plasma Membrane
(one of the major places to "dock" things)
- separation of cell interior from environment
- selectively permeable
- transport systems (food in, waste out)
- crucial metabolic processes
- respiration, lipid synthesis, etc.
- photosynthesis
- membrane receptors
- TM proteins
- detection of/response to chemicals
48
Bacterial Plasma Membrane cont.
- highly organized, asymmetric, flexible, & dynamic
asymmetric (what is facing outside is not always same as facing inside)
dynamic (have the ability to change, gives ability to perform differently)
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Bacterial Plasma Membrane Contents
- phospholipids
- proteins (2 main components)
- peripheral membrane proteins- loosely associated with cell membrane
- integral membrane proteins- in cell membrane
- "fluid mosaic model"
50
Phospholipids are Ampipathic
both a hydrophobic and hydrophilic end
51
Phosphatidylethanolamine
main phospholipid in bacterial cells
52
Uptake of Common Required Nutrients: Macroelements
macronutrients (most cell dry weight)
- C,O,H,N,S,P
- K+, Ca2+, Mg2+, & Fe2+/3+
- required in relatively large amounts
53
Uptake of Common Required Nutrients: Micronutrients
trace elements
- Mn, Zn, Co, Mo, Ni & Cu (small amounts)
- required in trace amounts
- enzyme cofactors
- often supplied in water or in media components
54
Growth Factors
essential cell components (or precursors); cell can't synthesize
- organic compounds
55
Classes of Essential Cell Components
- amino acids
- purines & pyrimidines
- vitamins
- function as enzyme cofactors
*cells cannot synthesize & required for enzyme activity
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Mechanisms for Uptake of Nutrients
- passive diffusion (some)
- facilitated diffusion
- active transport
- iron uptake
57
Passive Diffusion
- higher concentration to lower concentration
e.g. H2O, O2 and CO2
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Facilitated Diffusion
similar to passive diffusion
- not E dependent
- high concentration -> low concentration
- size of gradients impacts uptake rate
59
Facilitated Diffusion Differs from Passive Diffusion
- carrier molecules (permeases)
- smaller concentration gradient required
- transport of glycerol, sugars & amino acids
- more prominent in eukaryotic cells than in prokaryotic cells
- doesn't happen very often in prokaryotic cells
60
Facilitated Diffusion
- rate increases more rapidly and at a lower concentration
- rate reaches plateau
- carrier saturation effect
- (permeases) if there are 5 molecules inside cell, you cannot take anything more than 5 in until ones inside are fully saturated
- high concentration gradient, high rate of transport
- more outside, faster the process
61
Active Transport
- against concentration gradient
- energy-dependent process
- energy comes from ATP or proton motive force
- concentrates molecules inside cell
- accumulates molecules in case of "starvation"
- requires carrier proteins (permeases)
- carrier saturation effect
- example:
- ABC transporters
- secondary active transport
- group translocation
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ATP Binding Cassette (ABC) Transporters
- very well ubiquitously conserved
63
ATP Binding Cassette (ABC) Transporters: Components
- pore: 2 transmembrane domains
- nucleotide binding domains (ATP) - hydrolyzes ATP
-substrate (or solute) binding protein
- captures substance that is to be transported into cell
- periplasm
- deliver molecule to transporter
64
ATP Binding Cassette (ABC) Transporters: Molecules Transported
- sugars
- amino acids
- certain antibiotics
65
Secondary Active Transport
use ion gradients to cotransport substances
- protons; gradient generated by metabolic processes (electron transport chain)
- symport- two substances both move in the same direction
- antiport- two substances move in opposite directions
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Symporter
same direction
67
Antiporter
different direction
68
Cotransporters
can transport 2 things at once
69
Group Translocation
- molecules modified during transport
- energy-dependent processes
e.g. phospoenolpyruvate: sugar phosphotransferase system (PTS)
- transport of many carbohydrates
- e.g. mannitol, glucose
- components (e.coli/salmonella)
- PEP
- Enzymes I, IIA, IIB, IIC
- heat-stable protein (HPr)
- very common, widely distributed in bacteria
- many facultative anaerobes
- not in most aerobes
70
Iron Uptake
iron is very difficult to transport
- ferric iron (Fe3+) insoluble; uptake difficult
71
Iron Uptake: Siderophores
aid uptake, (sidero)- iron
- e.g enterobactin (e.coli)
- secreted; complexes with Fe3+
- complex transported
e.coli releases siderophores that change Fe into something (complex) that can be transported
72
Iron Uptake: Transport (Gm-)
- complex bound by receptor (outer membrane)
- periplasm: either...
- Fe3+ releases, enters directly, or
- complex transported via ABC
73
Bacterial Cell Wall
- rigid structure; surrounds plasma membrane
- consists of peptidoglycan (aka murein)
- synthesis inhibited by penicillin
74
Bacterial Cell Wall Functions
- shape
- protection (osmotic lysis)
- may contribute to pathogenicity
- may protect from toxic substances
75
Periplasmic Space Contains Periplasm
periplasmic space exists between plasma membrane & cell wall (Gm+)
plasma membrane & outer membrane (Gm-)
76
Periplasmic Enzymes
Gm-
Functions
- nutrient acquisition
- electron transport
- peptidoglycan synthesis
- modification of toxic compounds
77
Exoenzymes
Gm+
similar functions as periplasmic enzymes
78
Osmotic Lysis
- hypotonic solutions
- cell wall protects against osmotic lysis
- protects plasma membrane that swells from the water
79
Plasmolysis
- hypertonic solutions
- cell wall can't protect against plasmolysis
- as plasma membrane shrinks, cell wall cannot protect because it is exterior to membrane
80
Two Major Bacterial Groups
- Gm+ purple
- Gm- pink
- staining rxn probably due to cell wall structure
81
Bacterial Cell Wall & Gram Staining
- constriction of the thick peptidoglycan layer of Gm+ cells
- prevents loss of crystal violet during decolorization step
- therefore, purple
- thin peptidoglycan layer of Gm- bacteria does not prevent loss of crystal violet
- therefore, pink
82
Peptidoglycan
- polysaccharide formed from peptidoglycan subunits
- backbone: alternating sugars
- N-acetylglucosamine (NAG)
- N-acetylmuramic (NAM)
- provides agility & protection
83
Gram Positive Cell Envelope: Cell Wall
primarily peptidoglycan
- may also contain teichoic acids
84
Gram Positive Cell Envelope: Some Gm+ Bacteria
layer of proteins on surface of peptidoglycan
85
Gram Positive Cell Envelope: Lipoteichoic Acid
help connect cell wall and layer of peptidoglycans
86
Gram Positive Cell Envelope: Teichoic Acid
short molecules that help with connection between peptidoglycans
- specific to Gm+
87
Gram Negative Cell Envelope: Cell Wall
thin peptidoglycan layer surrounded by outer membrane
88
Gram Negative Cell Envelope: Outer Membrane
- lipids, lipoproteins, and lipopolysaccharide (LPS)
- no teichoic acids
89
Gram Negative Cell Envelope: Braun's Lipoproteins
connect outer membrane with peptidoglycan
90
Gram Negative Cell Envelope: Adhesion Sites
- not always present
- direct contact between plasma membrane and outer membrane
- may allow direct movement of material into cell
91
Gram Negative Cell Envelope: Lipopolysaccharides (LPS)
3 parts
- lipid A
- core polysaccharide
- O side chain (O antigen)
e.g. Salmonella typhimurium LPS
the more external side chain has the ability to protect and generate an immune response
92
LPS Functions: O Antigen
- protects from host defenses
- immunogenic
93
LPS Functions: Core Polysaccharide
contributes to negative charge on cell surface
94
LPS Functions: Lipid A
- stabilize outer membrane structure
- can act as an endotoxin
outer membrane loses integrity, LPS molecule is elixed into the host, releases into host when bacterium dies
95
Gram Negative Cell Envelope: Outer Membrane
- protective barrier
- more permeable than plasma membrane
- presence of porins and transporters
- porins: channels; small molecules (600-700 Da) *anything smaller than*
primers, has specificity in size but not type (of what is let in)
96
Layers Outside the Cell Wall: Capsules, Slime Layers, S-Layers
- protection from host defenses (ex phagocytosis)
- protection from harsh environmental conditions (ex desiccation)
- attachment to surfaces
- protection from viral infection or predation by bacteria
- protection from chemicals in environment (ex detergents)
- motility (gliding bacteria)
- protection against osmotic stress
97
Layers Outside the Cell Wall: Capsules
- usually polysaccharides
- well-organized; not easily removed
- resist phagocytosis (ex Strep pneumoniae)
98
Layers Outside the Cell Wall: Slime Layers
- polysaccharides
- diffuse, unorganized; easily removed
99
Layers Outside the Cell Wall: S-Layers
- not polysaccharides
- structured layers of protein or glycoprotein
- common among Archaea
100
Layers Outside the Cell Wall: Glycocalyx
- polysaccharide network
- another term for capsule/slime layer
(is not distinguished)- umbrella term
101
Archaeal Cell Envelope
- differ from bacterial envelope
- both molecular & organizational
102
Archaeal Plasma Membrane
- composed of unique lipids
- some have monolayer structure instead of bilayer structure
Why Monolayer?
archaea live in very harsh conditions. in high heat, a bilayer will break vs a monolater than can withstand harsh conditions
103
Archaeal Cell Wall
- Gm stain not useful, lack peptidoglycan
- chemical makeup varies
104
The Cytoplasmic Matrix
- substance between membrane and nucleoid
- ~70% H2O
- packed with ribosomes and inclusion bodies
- highly organized
- cytoskeleton-like organization/function
105
Bacterial Cytoskeleton
homologs of eukaryotic cytoskeleton components identified SEE TABLE ON SLIDE 67
106
Bacterial Intracytoplasmic Membranes: Plasma Membrane In-Foldings
folds toward cytoplasmic matrix
found in...
- many photosynthetic bacteria
- bacteria with high respiratory activity
may be aggregates of...
- spherical vesicles
- flattened vesicles
- tubular membranes
107
Bacterial Intracytoplasmic Membranes: Anammoxosome
- membrane-bound organelle
- found in anaerobic ammonia oxidation bacteria
- unique to Planctomycetes
108
Inclusions
aggregation of organic or inorganic material
types:
1. storage inclusions (specific to metabolism)
2. microcompartments
3. other inclusions
109
Storage Inclusions: Carbon
- glycogen inclusions
- glucose
- poly-beta-hydroxybutyrate (PHB) inclusions
- beta-hydroxybutyrate
110
Storage Inclusions: Phosphate
polyphosphate granules
111
Storage Inclusions: Sulfur
sulfur globules
112
Storage Inclusions: Nitrogen Storage
cyanophycin granules
- cyanobacteria
- large polypeptides (not from ribosomes)
- equal quantities of arg & asp
113
Microcompartments
- function other than metabolic stockpile
- not bound by lipid bilayer
ex) carboxysomes
- cyanobacteria, CO2- fixing bacteria
- concentration of CO2; enzyme localization
- ribulose- 1,5- biphosphate carboxylase (RUBISCO)
114
Other Inclusions: Gas Vacuoles
- some aquatic prokaryotes (ex: cyanobacteria, Halobacterium)
- buoyancy- vertical motility
- aggregates of gas vesicles- how high or deep in you are
- hollow cylindrical structures
115
Other Inclusions: Magnetosomes
- found in aquatic bacteria
- contain iron
- orient cells in magnetic fields (help bacteria find food)
116
Ribosomes
- complexes of protein and RNA
- protein synthesis
- associated with plasma membrane
- matrix ribosomes
- smaller than eukaryotic ribosomes
- prokaryotic ribosomes: 70 S
- large (50S): 5S + 23S + protein
- small (30S): subunit 16S + protein
S: unit that gives you an idea how far something will migrate through a concentration gradient
117
Nucleoid
- aka nuclear body, chromatin body, nuclear region
- ~60% DNA, 30% RNA; 10% protein
- location of chromosome
- usually 1/cell
- often circular; sometimes linear
- nucleoid proteins probably aid in folding
- differ from histones
- usually not membrane-bound
- irregularly shaped region
118
Plasmids
- usually small, closed circular DNA molecules
- extrachromosomal
- not required for growth and reproduction
- genes for selective advantage
ex) drug resistance
- can be laterally transferred
- transfer of plasmids from one molecule to another
- drug resistance spread
- widely used for molecular biological applications
119
External Structures
- pilli/fimbriae
-bacterial flagella
- archaeal flagella
120
Fimbriae (Fimbria)
- short, thin, hairlike, proteinaceous (made out of protein) appendages
- up to 1,000/cell
- attachment to surfaces
- type IV fimbriae: twitching motility
- have adhesions
121
Adhesions
proteins that help with adhesion to surfaces and help to move around
122
Sex Pili (Pilus)
- similar to fimbriae
- longer, thicker, less numerous (1-10/cell)
- required for mating (e.g. conjugation)
- specialized type of fimbriae
- create a bridge
- made of protein
123
Bacterial Flagella
- most motive bacteria (have flagella)
- thin, rigid structures
- up to 20 nano meters long
- being synthesized from the top
124
Patterns of Flagellar Arrangements
- polar
- monotrichous
- amphitrichous
- lophotrichous
- peritrichous
125
Flagellar Arrangements: Polar
at end of cell (pole of the cell)
126
Flagellar Arrangements: Monotrichous
one flagellum
127
Flagellar Arrangements: Amphitrichous
one at each end of the cell, @ each pole
128
Flagellar Arrangements: Lophotrichous
cluster at one or both ends
129
Flagellar Arrangements: Peritrichous
spread over entire surface
130
Bacterial Flagella: Ultrastructure (3 Parts)
1. filament
2. hook
3. basal body
131
Bacterial Flagella: Ultrastructure- Filament
hollow, rigid cylinder; flagellin (protein that makes up filament)
132
Bacterial Flagella: Ultrastructure- Hook
links filament to basal body
133
Bacterial Flagella: Ultrastructure- Basal Body
series of rings that drive flagellar motor, docks flagella into bacterial cell
134
Bacterial Flagella: Ultrastructure: Gram+ vs Gram - Cell
Gram +: 2 rings
Gram-: 4 rings
135
Bacterial Flagella: Flagellar Synthesis (Self Assembly)
- flagellin transported de novo through hollow filament
- similar to Type III secretion
- growth from tip
- length/weight of flagellin isn't identical through everything
136
Bacterial Flagella: Flagellar Movement
flagellum rotates
- counterclockwise: forward motion (run), flagellum behind bacteria
- clockwise: disrupts run (tumble)
direction is not random
137
Archaeal Flagella
- not as well-characterized
- differences
- > flagellin subunit type
- not hollow; thinner
- hook/basal
- rotation (Halobacterium)
- CCW: pulls cell
- CW: pushes cell
- doesn't rely on H+ motive force, but ATP hydrolysis
138
Motility: Spirochete Motility
- periplasmic axial fibrils: flexing/spinning movement
- mechanism not well-understood
flagella does not extend outside the cell
expansion & contraction
139
Twitching Motility
- pili (type IV) involved
- observed in group of cells (contracting)
140
Gliding Motility
- coasting along solid surfaces
- no known visible motility surfaces
- cyanobacteria, myxobacteria etc.
- 2 models
- polysaccharide secretion (expulsion of material from one end, propelling cell forward)
- adhesion complexes (mucus secretions rotate)
141
Chemotaxis
chemo- chemical
taxis- movement
- movement in response to a chemical
- movement towards/away from a chemical
- detected by cell surface chemoreceptors
142
Absence of Chemoattractant
random movement
- runs & tumbles
143
Chemoattractant Present
- directional movement
- caused by lowering the frequency of tumbles
144
Bacterial Endospore
- some Gm+ bacteria
- dormant (not metabolically active) ; resistant to numerous environmental conditions
- heat (boiling 1hr)
- radiation
- chemicals
- desiccation
145
Spore Structure: Exosporium
thin
146
Spore Structure: Spore Coat
thick
- impermeable; chemical resistance
147
Spore Structure: Cortex
peptidoglycan, helps with protection of core wall
148
Spore Structure: Core Wall
surrounds protoplast
- nucleoid
- ribosomes
- inactive
- very little water helps maintain inactive state
- hydration can make endospore become active
149
What Makes an Endospore so Resistant?
- calcium (complexed with diplicolinic acid)
- small, acid-soluble, DNA-binding proteins (SASPs)
- dehydrated core
- spore coat
- DNA repair enzymes
150
Sporulation
process of growing an endospore
- commences when growth ceases
- lack of nutrients
- complex multistage process
- can take hours to complete
- spores can last years to centuries
- process is reversible
151
Transformation of Spore to a Vegetative Cell (Reverse of Sporulation)
complex, multistage process
1. activation
2. germination
3. outgrowth
152
Activation
- prepares spore for germination
- often results from e.g heating
153
Germination
- spore swelling
- rupture/absorption of spore coat
- loss of resistance
- increased metabolic activity
154
Outgrowth
emergence of vegetative cell
