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Sem 2: Microbiology > Week 3 > Flashcards

Week 3 Flashcards

1
Q

Where does the word prokaryote come from?

A

The greek for prenucleus

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2
Q

Where does the word eukaryote come from?

A

The greek for true nucleus

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3
Q

What are prokaryote microorganisms?

A

Archaea and Bacteria

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4
Q

What are eukaryote microorganisms?

A

Algae, fungi and protozoa

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5
Q

What is the three domain system?

A

That there are three domains of life which are bacteria, archaea and eukaryotes which all decend from a common universal ancestor
This was proposed by Carl Woese

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6
Q

How can the three domains be distinguished?

A

By their cell wall

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7
Q

What is an overview of bacteria and their cell walls?

A

Bacteria are prokaryotic cells. The cell walls of Bacteria, contain peptidoglycan

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8
Q

What are an overview of archaea and their cell wall?

A

Archaea are prokaryotic cells. The cell walls of Archaea contain pseudo-peptidoglycan. Archaea often live in extreme environment, include extreme halophiles or thermophiles

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9
Q

What is an overview of eukarya and their cell wall?

A

Eukarya have eukaryotic cells. Not all Eukarya possess cell walls. Cell walls from Eukarya that posess cell wall do not contain peptidoglycan

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10
Q

What is a key difference between prokaryotes and eukaryotes?

A

Prokaryotes: absence of internal compartmentalisation by membranes
Eukaryotes: presence of membrane bound organelles such as the nucleus, mitochondria and chloroplasts

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11
Q

What is a key feature of prokaryote cells?

A

High surface/volume ratio

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12
Q

What is an advantage of having a high surface/volume ratio?

A

bacteria can sense and respond quickly to their environment (despite lack of organelles)
Increased secretion and uptake

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13
Q

What is an example of the difference in surface area/volume ratio in prokaryotes to eukaryotes?

A

Staphylococcus aureus: 1 um diameter sphere
pid3/6=0.52 um3 volume
pid2=3.14 um2 surface
S/V ratio: 6

Human erythrocyte, 10 m diameter sphere
pid3/6=520 um3 volume
pid2=314 um2 surface
S/V ratio: 0.6

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14
Q

What is the size of most bacteria?

A

Comparison of sizes of a variety of prokaryotes. Most known prokaryotes have cell diameters in the range of 0.5–2 µm

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15
Q

What is an example of a small bacteria?

A

haemophilus influenzae
0.25 x 1.25 um

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16
Q

What is an example of a large bacteria?

A

Oscillatoria (cyanobacteria)
8 x 50 um

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17
Q

What is an overview of the largest bacteria ever discovered?

A

Epulopiscium fishelsoni
Found in the intestinal tracts of surgeon fish
~ 2000 um long, 1000x longer than the average bacteria

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18
Q

What does a typical bacterium typically consist of?

A

cytoplasmic membrane within a peptidoglycan cell wall
Fluid cytoplasm contains the chromosome (nucleoid) and numerous ribosomes

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19
Q

What is an overview of the nucleoid?

A

The DNA is not surrounded by a nuclear membrane (no nucleus)
Single circular chromosome (few exceptions)

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20
Q

How large is E.coli DNA compared to an E.coli cell?

A

E.coli DNA length ~1400um E.coli length ~3 um

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21
Q

How is DNA packages in bacteria?

A

histone like proteins (HNS, HU)
Dps proteins
SASP-s in spores

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22
Q

How many ribosomes are their in a bacteria cell?

A

~15000 per cell

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23
Q

What is the difference between eukaryotes and prokaryotes molecular biology?

A

Eukaryotes: transcription in nucleus, translation takes place in the cytoplasm
Prokaryotes: transcription and translation take place in the cytoplasm: ribosomes start translation on RNA as it is being transcribed

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24
Q

What is the cytoplasmic membrane made out of?

A

Structure of a phospholipid bilayer. The cytoplasmic membrane is about 8 nm wide

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25
Q

What is the function of the cytoplasmic membrane?

A

Permeability Barrier
Generation of proton motive force

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26
Q

How does the cytoplasmic membrane act as a permeability barrier?

A

Only small, uncharged, hydrophobic molecules can pass through by diffusion
Protein Anchor
Transport, generation of energy, chemotaxis

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27
Q

What is different about Archaean cell membrane and bacteria membrane

A

Ether link - Archaea Ester link in bacteria
Branched hydrocarban -Archaea unbranched in bacteria

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28
Q

What are examples of storage molecules in bacteria?

A

C: poly-hydroxybutyrate, glycogen
P: polyphosphate granules

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29
Q

What bacteria produces poly-hydrobutyrate?

A

Ralstonia eutropha

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30
Q

What is the rough structure of poly-hydrobutyrate?

A

Poly-b-hydroxybutyrate (PHB). (a) Chemical structure of PHB, a common poly-b-hydroxyalkanoate. Other alkanoate polymers are made by substituting longer-chain hydrocarbons for the –CH3 group on the b carbon

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31
Q

What is a key trait about poly-hydrobutyrate?

A

Biopolymer with similar properties than synthetic polymers

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32
Q

What is a problem with synthetic polymers?

A

Synthetic polymers are often generated from Hydrocarbons (non-renewable energy source) non-biodegradable

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33
Q

Why can ploy-hydrobutyrate be used insted of biopolymers?

A

Renewable
BIODEGRADABLE (generating water and CO2)

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34
Q

What is an overview of gas vesicles?

A

Made of proteins
Gas permeable, but not water permeable allowing for control of floating properties
Occur in five phyla of the Bacteria and two groups of the Archaea

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35
Q

What are ges vesicles made from?

A

GvpA associates with GvpC, to build up gas vesicles, hollow protein structures. GvpA makes up most of the structure, as so called “ribs”, rigid β-sheets, whereas GvpC stabilizes the vesicle against collapse by crosslinking as α-helices

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36
Q

What is the function of magnetosomes?

A

They help orient bacteria

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37
Q

What is key in determining the function and structure of magnetosomes?

A

MamK (actin homologue) controls the organisation of magnetite particles in magnetosomes

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38
Q

What is the function of magneto-taxis?

A

Magneto-taxis in the northern (NH) and southern (SH) hemispheres aids cells in efficiently finding their optimum oxygen concentration ([O2]) at the microaerobic oxic–anoxic transition zone (OATZ) in water columns.

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39
Q

What is the difference between magento-taxis in the different hemispheres?

A

Polar magneto-tactic cells in the NH and SH to have opposite magnetic polarity due to the earths magnetic field working in the opposite direction

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40
Q

How do bacteria in the northern hemispheres travel up?

A

In both hemispheres, cells on the oxic side (northern hemisphere) of the OATZ swim down along the geomagnetic field lines by rotating their flagella counterclockwise (CCW)/ They rotate the flagella clockwise swim up the geomagnetic field lines

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41
Q

How do bacteria in the southern hemispheres travel up?

A

Those on the anoxic side (southern hemisphere) swim up along Bgeo by rotating their flagella clockwise (CW). The swim down by rotating flagella counterclockwise

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42
Q

What are the two phases of gram positive bacteria?

A

sporulation -formation of endospores
germination- return to vegetative growth

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43
Q

What are key features of endospores?

A

No metabolism
Extremely resistant to extreme environment (heat, desiccation, radiation, acids, chemical disinfectants)
Thick coat, DNA, few ribosomes, few enzymes
May lay dormant for thousands of years, then germinate in the presence of water and nutrients
Made in adverse conditions like the lack of nutrients.

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44
Q

What are the two main phases of vegetative cycle?

A

Growth - new daughter cells grow
Medial division - binary fission to produce daughter cells

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45
Q

What are the maun stages of endospore formation?

A

Polar division
Asymmetric cell division
Engulfment
Cortex
Spore coat
Maturation, cell lysis
Germination (when conditions return to habitable)

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46
Q

What are examples of bacteria that can form endospores?

A

Bacillus, Clostridium (Bacillus anthracis, Clostridium botulinum, Clostridium difficile)

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47
Q

How much water is in dormant cells?

A

Dormant cell: 15% water vs 70% in normal cells

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48
Q

What is the function of the flagellum?

A

Responsible for bacterial movement
Rotation of the flagella results in a propeller motion that moves the bacterial cells forward

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49
Q

What are the different types of flagellum?

A

Monotrichous - single flagellum at pole
Amphitrichous - a single flagellum on each opposite end
Lophotrichous - multiple flagella located at the same point
Peritrichous - multiple flagella around the body

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50
Q

How do Petrichous bacteria move around?

A

If spin counterclockwise the flagella bundle together and move the bacteria forward
If spin clockwise the flagella are pushed apart creating a spinning movement

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51
Q

How do mono or Lophotrichous bacteria move?

A

Counterclockwise rotation bacteria move forward
Clockwise rotation bacteria move backwards

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52
Q

What are an overview of Pili?

A

more numerous than flagella (10-250 per cell)
shorter than flagella ~1 micrometer
function: attachment or sex (occasionally motility)

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53
Q

What is an overview of Axial filaments?

A

Also called Endoflagella
Periplasmic – between cell wall and outer sheath
in spirochetes
Anchored at one end of a cell
Rotation causes cell to move – like a corkscrew

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54
Q

What are glycocalyx coat?

A

complex carbohydrate
polysaccharide + protein= glycoprotein coat
protein coat

55
Q

What are firmly and loosely attached coat?

A

Firmly - Capsule
Loosely - Slime

56
Q

What are the functions of glycocalyx?

A

Protection against:
- drying
- phagocytosis
- buffer between cell and environment
Adhesion
Cell-cell communication
Modulation of immune responses
Pathogenicity

57
Q

What are slime layers?

A

Meshwork may be a loose structure that is easily washed off

58
Q

Where are slime layers a problem?

A

Industry where bacteria in pipes produce huge amounts of slime to coat the inner surfaces of pipes and retard fluid flow

59
Q

What are capsules?

A

The coating of polysaccharide (sometimes proteins) that are firmly attached to the bacterial cell and does not wash off easily

60
Q

Where can capsules be seen?

A

As they do not wash off they can be seen in Gram stains

61
Q

What are biofilms?

A

Matrix-enclosed bacterial populations adherent to each other and/or to surface or interfaces with a self-produced extra-cellular matrix

62
Q

How present are biofilms?

A

In the environment most bacterial population are part of biofilms

63
Q

What is required for biofilm to be buildt?

A

Surface (solid-liquid or gas-liquid interface)
Moisture
Nutrients

64
Q

How is the biofilm buildt?

A

Free swimming bacteria undergo reversible adsorption on the substratum
Production of polysaccharide
Maturation of biofilm
Detatchment

65
Q

How are multispecies biofilms made?

A

Primary colonisers bind to substrate and divide
They form an extracellular polymeric substance which attracts secondary colonisers which then divide creating a mature multispecies biofilm

66
Q

What are the properties of biofilms?

A

Biofilm communities can be formed by a single bacterial species, but in nature biofilms almost always consist of rich mixtures of many species of bacteria, as well as fungi, algae, yeast and protozoa

67
Q

How do biofilms for in the sea?

A

Bacterial cells settle onto hard surface
Cell proliferate and secrete slime, forming a biofilm some cells detach
Protists grave on bacteria
If biofilm big enough, large organisms can attach to it

68
Q

What is an overview of extracellular polymeric substance?

A

Biofilms are held together by EPS : Extracellular Polymeric Substance, which often contains extracellular polysaccharides (slime).
This slime layer of EPS and bacteria entraps particulate materials such as clay, organic materials, dead cells and precipitated minerals, adding to the bulk and diversity of the biofilm habitat.

69
Q

What is the ecology of biofilms?

A

Some of the cells within the biofilm produce EPS that will act as a “glue” to generate complex, 3D structures
The biological diversity of the community may continue to increase as the biofilm attracts the attachment and growth of other organisms

70
Q

What are the characterisation of biofilms?

A

Gene expression is different in the biofilm compared to the free living (planktonic) bacteria
In the biofilms cells can co-ordinate their behaviour by intercellular communication via signalling molecules

71
Q

What are the benefits of biofilms for bacteria?

A

Nutrient utilisation
Decrease number of bacteria at threat from stresses
Even when biofilms are treated for prolonged periods of time or with elevated antimicrobial concentrations, a small fraction of the population persists
Higher frequency of formation of persister cells (can help survive antibiotics)

72
Q

What are beneficial biofilms?

A

Bioremediation of waste water treatment plants
Healthy gut flora

73
Q

How can biofilms increase infection?

A

Mixed biofilms on the artificial surface of catheters or other implants.

74
Q

How can biofilms play a role in ongoing infections?

A

Biofilms play a role in Bacterial Endocarditis (infection of the inner surface of the heart and its valves).
Biofilms form frequently in patients with Cystic Fibrosis (a chronic disorder resulting in increased susceptibility to serious lung infections).
Biofilms also play a role in Legionnaire’s disease (an acute respiratory infection resulting from the aspiration of clumps of Legionnella biofilms detached from air and water heating / cooling and distribution systems).

75
Q

How can biofilms impact morphology of biofilms?

A

Due to the morphology of biofilms, bacteria capable of forming them are highly resistant to antibiotics, making treatment very difficult.

76
Q

What can prevent biofilm formation?

A

Block formation
Coat surface preventing attachment
Dissolution of biofilm matrix
Deliver signal blockers
Induce detachment

77
Q

What is quorum sensing?

A

Regulation of gene expression in response to fluctuations in population density.
Single bacterium <—-> A large group of bacteria ( Quorum)
(A way for bacteria to count their numbers)

78
Q

What is the symbiotic relationship between Vibrio fischeri and bobtail squid?

A

V. fischeri (Gram-negative bacterium) lives in the light-sensing organs of the bobtail squid, which relies on V. fischeri to calculate the light (moon) shining from above and emit exactly the same amount of light downward, masking the squid from predators swimming beneath them

79
Q

What happens to the Vibirio fischeri in the bobtail squid everyday?

A

Each dawn, the squid evict all their V. fischeri to prevent overpopulation. During the day, the bacteria recolonize the light-sensing organ and detect a fresh quorum, once again ready to camouflage the squid by night.

80
Q

What are the process for light emission in Vibrio fischeri during quorum sensing?

A

LuxI: produces the signal molecule (often called autoinducer, AI)
LuxR: transcriptional activator
Upon binding AI, LuxR activates a set of genes including the lux genes for bioluminescence
Common in GRAM negative bacteria

81
Q

What is an overview of gram-negative bacteria quorum signalling molecules?

A

Acyl homoserine lactine autoinducers
The way it gets acetylated is the r group of the molecule

82
Q

What is an overview of gram-positive bacteria quorum signalling molecules?

A

Oligopeptide autoinducers

83
Q

What are the two domains of the bacterial components?

A

H: His of a sensor kinase
D: Aspartate of the response regulator

84
Q

How are the oligopeptide autoinducers grown?

A

A specific precursor peptide is produced. The precursor peptide is modified, processed, and an ATP-binding cassette (ABC) exporter complex secretes the mature oligopeptide autoinduce

85
Q

What happens to the oligopeptide autoinducer?

A

The oligopeptide autoinducer accumulates as the cells grow. At high cell density, the autoinducer is detected by a two-component signal transduction system

86
Q

What recognises the oligopeptide autoinducer sensor proteins?

A

The sensor kinase protein recognizes the autoinducer and subsequently autophosphorylates at a conserved histidine residue (H). The phosphoryl group is transferred to a cognate response regulator protein, and this protein is phosphorylated on a conserved aspartate residue (D)

87
Q

What happens to the phosphorylated response gene regulated by oilopeptide autoinducer?

A

The phosphorylated response regulator binds to specific target promoters to modulate the expression of quorum sensing regulated genes. P denotes that the mechanism of signal transduction is by phosphate transfer between the regulatory elements

88
Q

What are the domains of the sensor His Kinase?

A

Input domain and Autokinase
Input domain sends signal to Autokinase which then phosphorylation a histodine from ATP

89
Q

What domains and funcitons of the response regulator?

A

Regulator domain and output domain
The phosphate from the histodine goes to the regulator domain
Output domain is then activated helping transcription of specific gene

90
Q

What is the difference between signalling in Gram positive and gram negative bacteria?

A

The siganalling molecule is made by Lux1 enzyme in G.negative compared to be translated and modifies into protein in gram positive
Gram negative molecule can leave cell through diffusion where as Gram positive molecule needs transport system
Gram negative molecule can reenter cell whereas gram positive cant so generates a phosphorylation cascade when binds to receptor molecule

91
Q

How do pathogens use quorum sensing?

A

The bacteria appear relatively innocuous as they quietly grow in number.
When their population reaches a certain level, instant changes occur in their Behavior, Appearance, Metabolism
These changes culminate in an infection that can ambush and overwhelm our immune system defenses.

92
Q

What is an overview of Quoram sensing in Pseudomonas aeruginosa?

A

P. aeruginosa (Gram negative) uses a hierarchical quorum sensing circuit to regulate expression of virulence factors and biofilm formation

93
Q

What is the mechanism for quoram sensing in Pseudomonas aeruginosa?

A

lasR and lasI proteins
lasi synthesise autoinducer 1
AI1 then binds to lasR proteins activating gene expression for first line host attack genes

94
Q

What happens in quoram sensing when the lasR and AI1 complex is formed?

A

This triggers another set of genes to code for rhiR and rhii
rhii synthesise autoinducer 2
AI2 then binds to rhiR proteins activating gene expression for second line host attack genes

This complex targets its own complex promoting its own gene so its called an autoinducer

95
Q

What Virulence Factors Associated with Pseudomonas aeruginosa?

A

Lipopolysaccharide: Endotoxin activity
Pyocyanin: stimulates inflammatory response, mediates tissue damage
Exotoxin A: Inhibition of protein synthesis produces tissue damage
Elastase: Destruction of elastin containing tissues (blood vessels, lung tissue), collagen, immunoglobulin etc
Alkaline protease: Tissue destrucyion, inactivation of interferon and tumor necrosis factor-alfa
Rhamnolipid: Heat-stable hemolysin, inhibits pulmonary ciliary activity

96
Q

What are examples of bacteria and there quorum sensing proteins?

A

V.fischeri - Lux1 - Gram negative
P.aeruginosa - rhi1 - gram negative
B.subtilis - comX - gram positive
B.subtilis - CSF - gram positive
AI-2 universal language

97
Q

What is an example of bilingual quorum sensing?

A

Vibrio harveyi
AI-1 speaks language unique to Vibrio harveyi
AI-2 molecule speaks universal quorum sensing bacteria

98
Q

What is an overview of bacteria shapes?

A

Average size: 0.2 -1.0 µm  2 - 8 µm
Basic shapes:
1. spiral
2. rod
3. spherical

99
Q

What are unusual bacterial shapes?

A

Star-shaped Stella
Square Haloarcula
Most bacteria are monomorphic a few are pleomorphic

100
Q

What are main names for bacterial shapes?

A

Pairs - diplo - diplococci
Clusters - staphyl - staphylococci
Chains - strepto - streptococci

101
Q

What are examples of bacterial genus and there shape?

A

Bacillus - rod
Vibrios - curved rods
Streptomycetes - filamentous bacteria

102
Q

What causes bacterial cell shape?

A

Genetically determined
Cell wall (exocytoskeleton)
Strip the cell wall –> spheroplast/ protoplast
Genes involved in cell wall synthesis
bacterial cytoskeleton

103
Q

What is an overview of the bacterial cell wall?

A

Bacterial cell wall serves to give the organism its size and shape as well as to prevent osmotic lysis.

104
Q

What is the function of peptidoglycan?

A

Peptidoglycan confers rigidity to bacterial cell walls.

105
Q

What makes up peptidoglycan?

A

Backbone of alternating sugars
- N-acetylglucosamine (NAG)
- N=acetylmuramic acid (NAM) - unique
Joined by beta 1,4 lysozume-sensitive bond

106
Q

What amino acid side chains on NAM?

A

D amino acids
Diaminopimelic
(L amino acids in human cells)
Different bacteria have different side chains

107
Q

What makes up gram positive cell wall?

A

Thick peptidoglycan (60-90% of wall)
Interwoven teichoic acids (acidic polysaccharides)
Surface studded with proteins
No lipids present in the cell wall

108
Q

What is allowed through the gram positive cell wall?

A

Molecules pass freely through peptidoglycan so it does not trap molecules unless they are tethered to cell membrane or wall

109
Q

What makes up gram negative cell wall?

A

2 layer wall:
1. thin layer of peptidoglycan 10-20% of wall
2. outer membrane – permeability barrier

110
Q

What is the periplasm?

A

Gelatinous material between the outer membrane, peptidoglycan and cytoplasmic membrane.
Contains proteins needed for transport of material to and from cells.

111
Q

What makes up the outer membrane of a gram negaitve bacteria?

A

Phospholipid bilayer
Lipopolysaccharide (LPS): lipidA is embedded in outer membrane, polysaccharide extends outward from surface
Surface of membrane is studded with proteins

112
Q

What is the permiabilty of the outer membrane of a gram negative bacteria?

A

The membrane is semi-permeable containing protein channels like porins

113
Q

What is an overview of Lipopolysaccharide (LPS)?

A

Made from O-specific polysaccharide, core polysaccharide, Lipid A
Only in gram negative bacteria – link to pathogenicity: endotoxin
Part of the outer membrane

114
Q

What is an overview of mycobacterium and nocardia?

A

Gram-positive cell wall structure with lipid mycolic acid
Pathogenicity and high degree of resistance to certain chemicals and dyes
Basis for acid-fast stain used for diagnosis of infections caused by these microorganisms

115
Q

What is an overview of mycoplasma?

A

Some have no cell wall
cell wall is stabilized by sterols
pleomorphic

116
Q

What is an overview of cell wall of archaea?

A

Lack peptidoglycan
pseudo-peptidoglycan

117
Q

What is an overview of pseudo-peptidoglycan?

A

Instead of NAM (N-acetyl muramic acid) Archaea have :
N-acetyl talosaminuronic acid (NAT)
Archaea have no D-amino acids in their cell wall

118
Q

How does the cell wall grow?

A

NAM and NAG are synthesized in the cytoplasm
Links in the peptidoglycan have to be broken
New peptidoglycan monomers (NAM-NAG dimer) inserted
Peptide crosslinks resealed

119
Q

What is an overview of NAM and NAG are synthesized in the cytoplasm?

A

Attached to membrane carrier molecule called bactoprenol
Transported across the cell membrane

120
Q

What is an overview of Links in the peptidoglycan have to be broken?

A

Autolysins: break glycosidic bonds and peptide cross-bridges

121
Q

What is an overview of New peptidoglycan monomers (NAM-NAG dimer) inserted?

A

Using Transglycosidase enzymes

122
Q

What is an overview of Peptide crosslinks resealed?

A

Transpeptidase enzymes: penicillin binding proteins (PBPs) (inhibited by penicillins)

123
Q

What is an overview of the bacterial cytoplasm?

A

Four main types of cytoskeletal elements:
microtubules, composed of tubulin
microfilaments, composed of actin
intermediate filaments
molecular motors

124
Q

What are the elements of bacterial cytoskeleton?

A

Tubulin homologue: FtsZ
Actin homologue: MreB, Mbl proteins; ParM, MamK
Intermediate filaments: CreS
Molecular motors – not found in bacteria

125
Q

What is the function of actin?

A

Actin in eukaryotes is involved in many processes, including locomotion, cell growth, and cytokinesis

126
Q

What is the function of Mreb and Mbl?

A

MreB and Mbl (MreB like) proteins function in cell growth and shape
mreB, mecillinam resistance gene identified in Escherichia coli (rod shape)
mreB mutants are spherical while mbl mutants are deformed

127
Q

What happens to Mreb in the presence of ATP or GTP?

A

MreB polymerises into filaments in the presence of ATP or GTP

128
Q

How does MreB direct cell shape?

A

MreB direct the cell shape by localizing the proteins in a “peptidoglycan factory”

129
Q

What is the process for localising the proteins in a peptidoglycan factory?

A

MreC is required for the spatial organization of components of the peptidoglycan synthesis holoenzyme in the periplasm
MreB directs the localization of a precursor synthesis proteins in the cytosol

130
Q

How common is MreB?

A

among the 100 bacterial genomes, a striking correlation between nonspherical shape and the presence of at least one MreB homologue (B. subtilis has 3)
The gene has been lost in some of the bacteria such as the cocci

131
Q

What are examples of rod shape bacteria that dont have MreB?

A

Agrobacterium/Rhizobacterium and G(+) group of Mycobacterium/Corynebacterium do not contain mreB homologue

132
Q

Where does most cell wall grow in rod shaped bacteria?

A

Part of the cell wall synthesis takes place throughout the entire cell length (alongside MreB cables) eg Escherisca Coli

133
Q

Where does some cell wall growth occur in rod shaped bacteria?

A

Part of the cell wall synthesis takes place at the poles (NO MreB cables) eg Corynebacterium diptheriae

Sem 2: Microbiology (12 decks)

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