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Microbiology > 2. Cell Structure And Microscopy > Flashcards

2. Cell Structure And Microscopy Flashcards

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1
Q

Fill in the blanks HOE

A
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2
Q

Compound Light Microscopes

A
  • Use visible light to illuminate cells
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3
Q

Bright-field scope

A
  • Type of light microscope
  • Visualized by the differences in contrast between specimen and surroundings
  • Two sets of lenses from the image: objective lens (10x-100x) and ocular lens (10x-20x)
  • Max: 2000x
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4
Q

Fill in the blanks for a bright-field scope

A
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5
Q
A
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6
Q

Magnification

A

the ability to make an object larger

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7
Q

Resolution

A

the ability to distinguish 2 adjacent objects as seperate and distinct (limit of resolution for light microscope is about 2 mewm/200 nm

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8
Q

Microscope vs microscopy vs micrograph

A

microscope: object, microscopy: action, micrograph: resulting image

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9
Q

Calculating magnification

A

ocular x objective

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10
Q

How does resolution work?

A
  1. Two points can be distinguished if they are atleast .2 mewm apart
  2. light must pass between two points for them to be viewed as seperate objects
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11
Q
A
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12
Q

As wavelength decreases, resolution..

A

improves
- because the shorter the wavelength the easier it is to fit through

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13
Q

How to improve contrast in light microscopy

A

Staining!

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14
Q

How does staining work?

A
  • Using dyes that are organic compounds, they bind to specific cellular materials
  • Some microbes already are pigmented (ex. chloropyll make a microbe green)
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15
Q

Examples of common stains and their colours

A

Methylene blue - blue
Safranin - pink/red
Crystal violet - purple

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16
Q

Chromophore

A

charged portion of a dye

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17
Q

Simple staining

A

One dye used to colour specimen

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18
Q

Basic dye vs acidic dye in simple staining

A

Basic - positively charged chromophore - binds to negatively charged molecules on cell surface
Acidic - negatively charged chromophore - repelled by cell surface - stains background - good for looking at cell shape and size

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19
Q
A
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20
Q

Differential stains

A

gram stain - separates bacteria into 2 groups based on cell wall structureg

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21
Q

Gram positive vs gram negative in differential stains

A

gram positive: cells that retain a primary stain (purple)
gram negative: cells that lose the primary stain (take colour of counterstain - red/pink

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22
Q
A
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23
Q

Acid fast stain

A
  • for acid fast bacteria
  • detects mycolic acid in the cell wall of mycobacterium
  • mycobacterium - retains a primary stain (pink)
  • everything else - colour of counterstain (blue)
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24
Q

Endospore stain

A

internal structures and super resistant to killing
- endospore - retains primary - green
- cells - counterstained - pink

  • bacillus athracis
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25
Q

Disadvantages to stains

A

it kills the cells because its being dyed and heated - so we can’t use it for motiltiy

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26
Q

Phase-contrast microscopy

A
  • phase ring amplifies differences in the refractive index of cell and surroundings - doesn’t change the bacteria
  • used for live samples
  • dark cells with a light background
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27
Q

Dark field microscopy

A
  • less common
  • specimen is illuminated with a hollow cone of light
  • only refracted light enters the objective
  • specimen appears as a bright object on a dark background
  • used to observe bacteria that doesn’t stain well
  • triponema pallium
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28
Q

Fluorescence microscopy

A
  • used to visualize specimens that fluoresce
  • emit light of one color when illuminated with another colour of light
  • cells may fluoresce naturally (absorbs light at 430 nm - blue-violet and emits at 670 bm - red)
  • cells may fluoresce after staining with dye
    cyanobacteria
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29
Q

Differential Interference contrast (DIC) microscopy

A
  • uses a polarizer to create 2 distinct beams of polarized light
  • gives structures a 3D appearance (endospores, vacuoles, granules)
  • Structures not visible by bright-field microscopy are sometimes visible with this
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30
Q

Confocal scanning laser microscopy

A
  • uses a computerized microscope coupled with a laser source to generate 3D image
  • computer can focus the laser on single layers of the specimen
  • different layers can be compiled for a 3D image
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31
Q

Electron microscopy

A
  • uses electrons instead of photons (light) to image cells and structures
  • wavelength of electrons is much shorter than light - higher resolution
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32
Q
A
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33
Q

TEM

A

transmission electron microscope
- electron beamed focused on specimen by a condenser - magnets used as lenses
- electrons that pass through the specimens are focused by two sets of lenses - compound microscope
- electrons strike a fluorescent viewing screen
- goes through cell

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34
Q
A
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35
Q

Tem magnification, resolution, size, staining

A
  • high magnification and resolution (0.2 nm)
  • specimen is thin (20-60 bm)
  • must be stained with metals (lead or uranium), bind to cell structure to make it more electron dense, to see visualization of structures at molecule level
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36
Q
A
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37
Q

SEM

A
  • specimen is coated with a thin film of heavy metal (gold)
  • an electron beam scans the object
  • scattered electrons are collected by a detector and an image is produced
  • allows an accurate 3D image of the specimens surface
  • looks at surface of cell
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38
Q

Coccus

A

plural: cocci
spherical
ex) streptococcus pyogenee

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39
Q

Bacillus

A

plural: bacilli
rod shaped
ex) e.coli

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40
Q

Spirillium

A

plural spirilla
spiral shaped
ex) spirillum volutans

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41
Q
A
  1. cocci
  2. bacillus
  3. spirillum
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42
Q

Spirochete

A

corkscrew
ex) treponema pallidum

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43
Q

Budding and appendaged bacteria

A

looks like a balloon
ex) caulobacter crescentus
- has the long part of attachment

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44
Q

Filamentous bacteria

A

ex) streptomyces griseus

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45
Q
A
  1. spirochete
  2. budding and appendaged bacteria
  3. filamentous bacteria
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46
Q

What does morphology not predict

A

physiology, ecology, phylogeny

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47
Q

Selective forces in morphology

A
  1. optimization for nutrient uptake
  2. swimming motility in viscous environments or near surfaces
  3. gliding motility
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48
Q

Prokaryotic sizes and examples

A
  1. average - E.coli (1.0x3.0 mewm)
  2. very small - mycoplasma genitalium (0.3 mewm)
  3. very large - epulopiscium fishelsonii (80x600 mewm)
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49
Q

Advantages to being small

A

small cells have more surface area relative to cell volume than large cells (higher surface to volume ratio)
- support greater nutrient exchange per unit cell volume
- tend to grow and adapt faster than larger cells

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50
Q

Cellular organisms less than ___ in diameter are unlikely

A

0.25 mewm

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51
Q

Open oceans tend to contain ___

A

small cells (0.2-0.4 mewm in diameter)

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52
Q

Why are pathogenic bacteria small

A

they are missing genes - get these functions of issing genes from hosts

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53
Q

Membrane is made out of

A
  • phospholipid bilayer
  • hydrophobic: fatty acids point inward
  • hydrophilic: glycerol-phosphate and points to external environment
  • can exist in many different chemical forms as a result of variation in the groups attached to the glycerol backbone
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54
Q

Phospholipid structure

A

ester phospholipids:
- glycerol
- 2 fatty acids
- phosphate
- optional side chain
amiphipathic: has polar and non-polar characteristics
polar: molecule carries full or partial charge - hydrophilic
non-polar: molecule is uncharged - hydrophobic

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55
Q
A
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56
Q

How are these stabilized

A
  • 8-10nm wide
  • embedded proteins
  • stabilized by hydrogen bonds and hydrophobic interactions
  • Mg and Ca ions help stabilize the membrane through ionic bonds with negative charges on the phospholipids
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57
Q

Membrane proteins in gram negative

A

in gram-negative bacteria;
- interacts with proteins that bind substrates or process large molecules for transport
- interacts with proteins involved in important cell functions like energy-yielding reactions

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58
Q

Integral vs peripheral membrane proteins

A

integral: firmly embedded in the membrane
peripheral: one portion anchored in the membrane

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59
Q

Archaeal Membranes

A
  • ether linkages in phospholipids
  • archael lipids lack fatty acids - isoprenes instead
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60
Q
A
61
Q

Lipid monolayers and bilayers and heat

A

bilayer - not heat resistance
monolayer - heat resistance

62
Q

What type of prokaryote are lipid monolayers found

A

hyperthermophilic archaea- likes high temps

63
Q

Membrane functions

A
  1. surrounds the cell - seperates cytoplasm from environment
  2. highly selective permeable barrier - enables concentration of specific metabolites and excretion of wastes products (concentration gradient to represent the needs of the cell)
  3. protein anchor - holds transport proteins in place
  4. energy conservation - generation of proton motive force
64
Q

Carrier-mediated transport systems

A
  • shows saturation effect
  • highly specific
65
Q
A
66
Q

Uniporters, symporters, antiporters

A
  1. transport in one direction across the membrane
  2. cotransporters
  3. transport a molecule across the membrane while simultaneously transporting another molecule in the other direction
67
Q

Simple transport example

A

Lac permease of E.Coli
- lactose is transported into e coli by lac permease a symporter that moves 2 molecules (lactose and H+) across a membrane in the same direction
- energy-driven

68
Q

Group translocation example

A

phosphotransferase system in E. Coli
- sugar is phosphorylated during transport across the membrane
- moved glucose, fructose and mannose
- PEP donates a P to a phosphorelay system
- P is transferred through a series of carrier proteins and deposited onto the sugar as its brought into the cell

69
Q

ABC Transport systems

A
  • uptake of organic compounds and inorganic nutrients and trace metals
  • high substrate specificity - picky
70
Q

Gram-negative ABC transport system

A

periplasmic-binding proteins and ATP-driven transport proteins

71
Q

Gram-positive ABC transport system

A

substrate-binding lipoproteins (anchored to external surface of cell membrane) and ATP-driven transport proteins

72
Q

Cell wall in bacteria and archaea

A
  • outside the cell membrane
  • rigid
  • determines cell shape
  • not a major permeability barrier
  • porous to most small molecules
  • protects the cell from osmotic changes
73
Q

Functions of the cell wall

A
  • prevents cell expansion (protects from osmotic lysis)
  • protects against toxic substances (large hydrophobic molecules)
  • pathogenicity - helps evade host immune system and bacterium stick to surfaces
74
Q

Peptidoglycan

A
  • species of bacteria seperated into 2 groups based on gram stain
  • provides strength to cell wall
75
Q

Do archaea have peptidoglycan

A

Naur!!!

76
Q

Gram-positive vs gram-negative cell wall structure

A

Gram-negative: 2 layers - LPS and peptidoglycan
Gram-positive: 1 later - peptidoglycan

77
Q

What is peptidoglycan made of

A
  • A polysaccharide
  • N-acetylglucosamine
  • N-acetylmuramic acid
  • amino acids
  • lysine or diaminopimelic acid (DAP)
  • cross-linked differently in gram+ and gram-
  • forms glycan tetrapeptide
  • beta 1,4 linkage
78
Q

How can peptidoglycan vary

A
  • 100 different structures
  • vary in peptide cross-links or interbridge
79
Q

Is an interbridge present in gram-negative bacteria

A

naur!

80
Q

Gram-positive cell wall

A

90% peptidoglycan
- teichoic acids (acidic substances) embedded in cell wall

81
Q

Lipoteichoic acids

A

teichoic acids covalently bound to membrane lipids

82
Q

Peptidoglycan
- backbone formed of ___ and ___ connected by _____________
- crosslinks formed by _________
- peptidoglycan strand is ________ and allows for ______________ (It needs this to ____________)
- some cell walls can be _______ layers thick

A
  • backbone formed of NAM and NAG connected by glycosidic bonds
  • crosslinks formed by peptides
  • peptidoglycan strand is helical and allows for 3d crosslinking. it needs this to hold them together
  • some cell walls can be 50-100 layers thick
83
Q

prokaryotes that lack cell walls and what replaces their cell walls?

A
  • Mycoplasmas - sterols in cytoplasmic membrane
  • Thermoplasma - lipoglycans in membrane
84
Q

lipopolysaccharide layer

A
  • a lipid with many sugars
  • The outer membrane
  • Total cell wall contains 10% peptidoglycan
  • consists of core polysaccharide and O-polysaccharide
  • LPS replaces most of phospholipids in outer half of outer membrane
  • Lipid A (endotoxin) is toxic
85
Q

periplasm

A
  • space located between cytoplasmic and outer membrane
  • gel-like consistency
  • has many proteins
86
Q

porins

A

channels for movement of hydrophilic low-molecular-weight substances

87
Q

Bacteria outer membrane summary

A
88
Q

Cell wall and gram stain relationship

A
  1. Stained with crystal violet - it gets stuck inside cell
  2. Flushed with alcohol - + not extracted, - is extracted
  3. gram positive bacteria have thick cell walls - it becomes dehydrated during the alcohol step so pores in wall close and prevents colour from escaping
    gram negative bacteria - alcohol penetrates OM and colour is extracted from cell so its clear
  4. stained with safranin - + purple is darker than pink so u cant see it, - is stained pink and red
89
Q

Archael cell walls

A
  • no peptidogly
  • no outer membrane
  • instead they have pseudomurein
  • some archaea dont have pseudomurein
90
Q

What is pseudomurein composed of

A
  • polyscharride
  • N-acetylglucosamine
  • N-acetyltalosaminuronic acid
  • beta 1,3 linkage
91
Q

Differences in peptidoglycan and pseudomurein

A

Peptidoglycan:
- N-acetylmuramic acid
- beta 1,4 linkage
- structure has L and D
Pseudomurein:
- N-acetyltalosaminuronic acid
- beta 1,3 linkage
- structure it has L only

92
Q

S-layer

A
  • archaea cell wall type
    archaea and bacteria
  • proteins and glycoprotein
  • paracrystalline structure (hexagonal, tetragonal, trimer)
  • some archaea only have S-layer
93
Q

Why are archaea resistant to lysozyme and penicilin?

A

They lack peptidoglycan

94
Q

Cytoplasm

A

material bounded by plasma membrane

95
Q

Protoplast

A

PM and everything within
- macromolecules
- soluble proteins
- DNA and RNA

96
Q

Protein functions

A
  • enzymes that catalyze chemical reactions
  • transport proteins - move other molecules across membranes
  • structural proteins - help determine shape of cell and cell division
  • proteins are made of polypeptides (a long polymer of amino acids joined by peptide bonds)
97
Q

Nucleoid

A
  • region that containes genome
  • typical bacterial genome: single circular double stranded DNA chromosome
  • may have one or more plasmids - smaller circular dsDNA, self-replicating, carry non-essential genes (selective advantage)
  • DNA: carries genetic info of all cellsR
98
Q

Ribosome

A
  • site of protein synthesis
  • bacteria have 70s ribosome
  • 30s subunit (small subunit) - protein and 16s rRNA
  • 50s subunit (large subunit) - protein and 23s and 5s rRNA
  • cytoplasmic ribosome that make cytoplasmic proteins
  • PM associated with ribosomes - membrane proteins that are exported from the cellc
99
Q

Capsules and slime layers

A
  • expresses sometimes
  • polysaccharides and protein layers
  • think or thick
  • attachment to surfaces
  • protects against phagocytosis
  • resist drying out
100
Q

biofilm

A
  • community of bacteria associated with a surface
  • stronger together
101
Q

fimbriae

A
  • filamentous protein structures
  • stick to surfaces or form pellicles
102
Q

pili

A
  • filamentous protein structure
  • longer than fimbriae
  • surface attachment
  • gene exchange between cells (for better genes) - horizontal
  • type 4 pili for twitching motility
103
Q

cell inclusion bodies

A

visible aggregates in cytoplasm

104
Q

carbon storage polymers

A
  • poly-B-hydroxybutyric acid - lipid storage
  • glycogen - glucose polymer
105
Q

inorganic inclusions

A
  • polyphosphate granule - volutin - storage of phosphate and energy
  • sulfur globules - storage of sulfur used in energy generation
106
Q

magnetosomes

A
  • magnetic inclusions
  • intracellular granules that give the cell magnetic properties
  • allows it to orient itself in a magnetic field
  • bacteria migrate along earths magnetic magnetotaxis
107
Q

gas vesicles

A
  • give buoyancy
  • spindle-shaped, gas-filled structures
  • made of proteins
  • function by decreasing cell density
  • impermeable to water
108
Q

endospores

A
  • highly differentiated cells resistant to heat, harsh chemicals and radiation
  • hibernating stage of bacterial life cycle
  • ideal for dispersal via wind, water or animal gut
109
Q

how to kill endospore

A

autoclave - pressure and heat

110
Q

what kind of gram bacteria produces endospores

A

gram positive

111
Q

endospore growth

A
  • vegetative - capable of normal growth (metabolically active)
112
Q

protective features of endospores

A
  • Layers
    1. spore coat and cortex for protection against chemicals, enzymes, physical damage and heat
    2. two membranes - pearmeability barriers against chemicals
  • Core
    3. dehydrated - protects against heat
    4. ca-dipicolinic acid and SASPs (small acid soluble proteins) that protect against DNA damage
113
Q

What can endospores resist

A
  1. boiling for hours
  2. uv radiation
  3. chemical disinfectants
  4. drying
  5. age
114
Q
A

Stage 1. Asymmetric cell division
- DNA replicates
- identical chromosomes pulled to opposite ends of the cell

Stage 2. Septation
- divides cell into 2 unequal compartments - both have their own chromy
- forespore
- mother cell

Stage 3. Mother engulfs forespore
- forespore surrounded by 2 membrances

Stage 4. formation of the cortex
- thick layers of peptidoglycan form between 2 membranes
- highly cross-linked layer (core)
- loosely cross-linked layer (cortex)a

Stage 5. coat synthesis
- protein layers surround the core wall
- spore coat
- exosporium (found in some G+ and non-essential)
- protect the spore from chemicals and enzymes
- accumulates in spore; calcium, dipicolinic acid and small acid soluble proteins (SASPs) accumulate in the core to help stabilize DNA

Stage 6. endospore matures
- core is dehycrated
- 10-30% of a vegetative cells water content

Stage 7. mother cell is lysed
- mother cell disintegrates
- mature spore is released

115
Q

flagella

A
  • hollow protein filaments
  • for motility
  • must be stained to view
116
Q

monotrichous

A

single flagella
1. polar - on the side
2. sub polar on bottom or top

117
Q

amphitrichous

A

flagella at opposite ends

118
Q

lophotrichous

A

multiple flagella in a single tuft

119
Q

peritrichous

A

flagella distributed around the cell

120
Q

flagella structure

A
  1. filament
  2. hook
  3. basal body
121
Q

filament in flagella

A
  • helical protein 20 mewm long
  • composed of identical protein subunits - flagellin
122
Q

hook in flagella

A
  • flexible coupling between filament and basal body
123
Q

basal body in flagella

A

consist of central rod that passes through a series of rings
1. L - LPS layer
2. P - peptidoglycan
3. MS - membrane
4. C - cytoplasm - associated with membrane

124
Q

Energy in flagella

A

-energy to turn the flagella comes from the proton motive force (PMF)
- gradient of protons (H+) across the cytoplasmic membrane - high H+ on outside and low H+ on inside
- MOT proteins form a channel that allows H+ to move into cytoplasm
- flagellum turns like a propellar to drive cell forward

125
Q
A
126
Q

flagellar synthesis

A
  • several genes are required for flagellar synthesis and motility
  • MS ring is made first
  • other proteins and hooks are made next
  • filament grows from tip
127
Q

Peritrichous vs polar cells swimming motions

A

peri - move slowly in a straight line
polar - more more rapidly and spin more

128
Q

Gliding motility

A
  • flagella independent motlity
  • slower and smoother than swimming
  • needs surface contact
  • mechanisms: type 4 pili for twitching (ATP hydrolysis) and gliding specific proteins (proton motive force)
129
Q

Taxis

A

directed movement of cells in response to chemical or physical gradients

130
Q

chemotaxis, phototaxis, aerotacis, osmotaxis, hydrotaxis

A

chemo - response to chemicals
photo - light
aero - oxygen
osmo - ionic strength
hydro - water

131
Q

Example of chemotaxis

A
  • E.coli
  • bacteria repsonded to temporal not spatial difference in chemical concentration
  • run and tumble behavior
  • attractants and repellants are sensed by chemoreceptors
  • the net movement - run more and tumble less to attractant
132
Q

Measuring chemotaxis

A
  • Measured by inserting a capillary tube containing an attractant or a repellants in a medium of motile bacteria
  • seen under a microscope
133
Q

Eukaryote cell size

A
  • lower surface area to volume ratio
  • larger than pro
134
Q

Key differences in pro and euk

A
135
Q

Nucleus, chloroplast and mitochondria

A

nucleus - genetic info - multiple linear dsDNA chromosomes
chloroplasts - site of photosynthesis, chlorophyll, surrounded by 2 membranes, DNA and ribosomes (70s)
mitochondria - site of respiration and oxidative phosphorylation, surrounded by 2 membranes. DNA and ribosomes (70s)end

136
Q

Endosymbiotic Hypothesis

A

mitochondria and chloroplasts evolved from bacteria
1. semi-autonomous - make their own DNA
2. circular choromsomes that lack histones
3. 70S ribosomes
4. 2 membranes
5. outer membrane has porins

137
Q
  • mitochondria and chloroplast mostly related to and why
A

mitochondria - most closely related to Rickettsia, proteobacteria, obligate intracellular pathogens
chloroplasts - most closely related to cyanobacteria, blue green algae

Comparison of 16s rRNA gene sequences

138
Q

Viral genome, shape and size, strand number,

A
  • DNA or RNA - never both
  • single stranded or double stranded
  • circular or linear
  • can be in several pieces - segmented
  • genome size:
    small - 3.6 kb for ssRNA viruses (3 genes)
    largest 150kbp for some dsDNA viruses (>100 genes)
138
Q

Viruses

A
  • non-living so technically not a microorganism
  • acellular infectious particles
  • obligate intracellular pathogens
  • reproduce only inside living cell
  • lack independent metabolism
  • composed of at least 2 parts - nucleic acid genome (DNA or RNA) and protein code (capside) - nucleocapside
  • some viruses have an envelope
  • gets the rest of their parts from their host cell
139
Q

capsid

A

protein coat that surrounds the genome
- allows transfer of viral genome between host cells
- made of identical polypeptides - protomer
- helical capsids - protomers form a spiral cylinder, nucleic acid genome coiled inside
ex) tobacco

140
Q

icosahedral capsids

A

-regular geometric shape with 20 triangular faces
- symmetry
- protomers aggregate to form capsomeres

hpv

141
Q

binary capsids

A
  • geometric head with ana attached helical tail
  • genome is carried in a polyhedral head, helical tail is used to inject DNA into a host cell
    -t4 in ecoli
142
Q

Nucleocytoplasmic large DNA viruses

A
  • viruses with complex multi-layered structure
  • larger than some bacteria

-mimivirus

143
Q

envelope

A

a lipid bilayer surrounding the nucleocapsid that was acquired from the host membrance
- consists of host lipids and viral proteins - spikes
- flexible helical capsid, surrounded by an envelope
- 2 major spikes: hemaglutanin (H) and neuraminidase (N)

144
Q

viruses - host range

A
  • attach to specific receptors
  • viruses infect all domains of life
  • bacteriophage (phage) - viruses that infect bacteria
  • animal viruses - infect and multiply only inside of animal cells - causes benign tumors
145
Q

viruses - host range - how many attachments?

A
  • most viruses are specific to a single host species
  • virus must attach to specific receptors on the host cell surface - ex) HIV binds to CD4
    chemoreceptor on surface of some human immune system cells
  • some viruses infect more than 1 specie ex) influenza
146
Q

Viral replication cycle

A
  1. Absorption - attachment to host cell - involves specific receptors on the host cell surface
  2. Penetration and uncoating - entry into a host cell - bacteriophage (usually inject their nucleid acid into the cell) - leave the capside outside the cell as a ghost
  3. Synthesis of viral nucleic acids and protein - viral genes are expressed and viral proteins are synthesized - viral genome is replicated
  4. Assembly of new virions - viral proteins are assembled into capsids and then genomes are packaaged into nucleocapsids - viruses don’t reproduce by division
  5. Release of new virions by 1. naked viruses accumulare eventually lysing the host cell to release progeny - lytic infection or 2. enveloped viruses are usually released by budding - virions push through the cytoplasmic membrane without killing the host cell - persistent infection
147
Q

Entry by animal viruses

A
  • fusion with plasma membrane (envelope viruses only)
  • endocytosis - bidning to specific receptors triggers normal endocytic activity
  • once inside - the capside is removed - viral genome is released into the cell

neuraminidase allows new virions to exit the host cell
- hemagglutanin allows viruses to absorb to the next host

Microbiology (8 decks)

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