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Microbial Physiology > Exam 1 > Flashcards

Exam 1 Flashcards

1
Q

Components of Prokaryotic Cell

A

Envelope, cytoplasm, nucleoid

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2
Q

Components of Eukaryotic Cell

A

Chloroplast, cilium, endoplasmic reticulum, golgi, lysosome

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3
Q

Prokaryotic Cell Size

A

0.1 um - 0.5 mm (5000 fold range) length, most are only 1-2 um
500 fold range width

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4
Q

Eukaryotic Cell Size

A

10-100 um in length, 2-200 um in diameter

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5
Q

Surface-to-volume ratio

A

3/r

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6
Q

G+

A

Thick peptidoglycan layer

Teichoic and lipoteichoic acids provide stability

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7
Q

G-

A

Lipopolysaccharide layer, thin peptidoglycan

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8
Q

G- Cell Wall is made up of

A

Outer membrane, peptidoglycan layer

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9
Q

G- periplasmic space

A

Between cell wall and inner plasma membrane

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10
Q

Peptidoglycan components

A

Polysaccharide chains of NAG and NAM connected through B 1,4 linkages
Chains connected by short tetrapeptides of repeating amino acid enantiomers (L-ala, DAP, D-glutamic acid, D-alanine)

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11
Q

Regulation of Cell Wall

A

Autolysins: cleave peptide cross links
Transpeptidases: repair breaks and add additional peptidoglycan
Abundance and activity tightly controlled by the cell

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12
Q

Cell Wall Functions

A

Determines cell shape, resists intracellular pressure

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13
Q

S-layer

A

Made of repeating protein subunits (often single protein) that form a sheet-like structure
“liquid crystalline array”
Two dimensional
Pores

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14
Q

Fungal cell walls

A

Chitin, resembles peptidoglycan. Polymer of B-1,4 linked NAG
Cellulose. Polymer of B-1,4 linked glucose
Glucan. Polymer of alpha-1,6 linked glucode

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15
Q

Algal cell walls

A

Cellulose or pectin (polymer of galacturonic acid) or protein

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16
Q

Mycoplasma, Thermoplasma cell wall

A

Lacks cell wall, require environment where external solute concentration is similar to intercellular
Avoid turgor pressure

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17
Q

Bacterial and eukaryotic phospholipids

A

Use ester bond to couple glycerol and fatty acids

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18
Q

Archaeal phospholipis

A

Use an ether bond to couple glycerol and fatty acids

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19
Q

Hyperthermophilic archaea unique membrane

A

Lipid monolayer

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20
Q

Outer membrane is found in _____ and result in the ______

A

Gram - and gram variable, periplasm

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21
Q

Periplasm

A

More dilute than cytoplasm
Oxidized
Rapid exchange with environment
Contains hydrolytic enzymes (increases access to substrate, but retains them in close proximity to the cell)

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22
Q

What is the behavioral consequence of the periplasm?

A

G- secrete less protein into the environment than G+

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23
Q

Lipoprotein

A

Anchors outer membrane to the cell wall
Tail embedded in inner leaf of outer membrane
Protein component binds cell wall

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24
Q

LPS

A

Endotoxin, elicits fever in humans

Made of Lipid A, core polysaccharide and O-polysaccharide

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25
Q

O-polysaccharide

A

made of hexoses in repeating clusters (glucose, galactose, rhamnose and mannose), varies significantly between strains of bacteria. Important distinguishing marker

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26
Q

Core polysaccharide

A

Varies in composition between organisms

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27
Q

Lipid A

A

Lipid portion of LPS, ester-linked FAs coupled to a disaccharide of N-acetyl glucosamine phosphate

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28
Q

Gram Variable

A

Acid fast
Mycobacteria
Made of phospholipid combined with mycolic acids, not LPS
Porins present

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29
Q

Mycolic acid

A

Long chain fatty acids extending 70 or more carbons

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30
Q

Small molecule transport mechanisms

A

Simple diffusion, osmosis, facilitated diffusion and active transport

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31
Q

Group Translocation is found in

A

Prokaryotes, chemically modifies incoming molecule consuming energy

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32
Q

What type of transport is only found in eukaryotes?

A

Pinocytosis and endocytosis

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33
Q

Cytoplasm

A

90% water
Highly reducing
Protein thiol groups remain protonated, minimizing sulfhydryl bonds
pH is constant, near neutral

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34
Q

Prokaryotic cytoplasm

A

Not disorganized
Cryoelectron microscopy and biochemical/genetic analysis of protein complexes show that cellular processes occur in discrete locations, and involve the coordinated action of large complexes of proteins

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35
Q

What grows at pH

A

Archaea and possibly a few fungi

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36
Q

What grows at pH >10?

A

Bacteria and archaea

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37
Q

Eukaryotic cytoplasm

A

Complex
Contains nucleus and organelles
Facilitate movement of proteins and other molecules
Cytoskeleton

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38
Q

Cytoskeleton

A

Critical for cell division and movement

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39
Q

Crenarchaeal chromosomal organization

A

NAP (bacteria like)

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40
Q

Euryarchaeal chromosomal organization

A

Eukaryote like, histone proteins and nucleosomes

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41
Q

Primary transcript processing in Eukaryotes

A

Splice out introns, 5’-methylguanosine cap, 3’ polyadenylate tail

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42
Q

Prokaryotic ribosomal subunits

A

30S + 50S = 70S

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43
Q

Eukaryotic ribosomal subunits

A

40S + 60S = 80S

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44
Q

Prokaryotic 30S subunit

A

16S rRNA

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45
Q

Prokaryotic 50S subunit

A

23S and 5S rRNA

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46
Q

Proteasome

A

Multisubunit macromolecular structures that degrade proteins
Barrel shaped, central pore through which protein substrates pass during degradation
20-26S
Archaea (fewer proteins but higher copy number) and Eukaryotes (25 proteins)

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47
Q

Storage Bodies

A

Polyhydroxybutyrate inclusions
Carboxyl connected to carbon chain, R group determines type > CH3 = PHB
Nitrogen rich compounds
Lipids

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48
Q

Capsules

A 
Outside prokaryotic envelope
Glycocalyx or slime layer
Polysaccharides (or amino acids) that coat cells (type varies)
Escape from predation
Surface adherence
Virulence (escape phagocytosis)
Resistance to environmental extremes
Loss can lead to nonpathogenicity
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49
Q

Pilus

A

Also called fimbria
Made of pilins arranged in a helical array forming a long thin tube-like structure with a hollow central core
Interspersed with adhesins (enable attachment)
G- sex pilus allows conjugation
Loss can lead to nonpathogenicity

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50
Q

Flagellar Motor

A

Nanomachine
Rotate flagellum around axis
Made of Mot, Fli proteins, M and S rings, P and L rings

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51
Q

Flagellin

A

Protein subunits that make up flagellum

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52
Q

Bacterial vs Archaeal Flagella

A

Flagellin is similar among bacteria, but different in Archaea
Flagella evolved separately in the two groups

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53
Q

Flagellin is assembled at

A

The tip of the rod, not the base

Flagellin monomers pass through the hollow core where they are assembled by cap proteins

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54
Q

Assembly of flagellum

A

Insertion of M and S rings, motor proteins, then P and L rings and finally the hook

55
Q

Mot

A

Rotation of the motor is caused by mot (motor) proteins
Use proton gradient
Size of the gradient is proportional to rate of rod movement
1,000 proton required for each rotation

56
Q

Fli

A

Control direction of rotation, reversible depending on intracellular signals concerned with environmental conditions

57
Q

Oligotrophy

A

Prefer conditions of limited nutrient availability
Do not exhibit unrestricted growth under nutrient excess conditions, divide at very slow rates
Open ocean

58
Q

Copiotrophy

A

Exhibit unrestricted growth in response to conditions of nutrient excess
Model systems, achieve high densities in laboratory culture

59
Q

Colony with diameter of 1 mm

A

10^8 cells (100 million)

60
Q

Spectrophotometry can detect

A

Populations 10^7 cells or greater

61
Q

Changes within a colony

A

Differences in oxygen, light availability, pH, nutrients and osmolarity

62
Q

Death Phase

A

Not obligatory, not terminal step in pathway of differentiation
Microbes can stay in growth phase indefinitely
Stationary cells can transition to lag and then growth phase to avoid death phase

63
Q

Quorum Sensing

A

Signal transduction
Environmental or biological cue that is communicated to cells and stimulates changes in gene expression
Bacterial prokaryotes and fungal eukaryotes
Can results in macroscopic events

64
Q

Quorum sensing molecules

A

Homoserine lactones

Small peptides

65
Q

Flourescence

A

Luciferase encoded by lux genes
Oxidizes long chain aliphatic aldehydes and flavin mononucleotide in the presence of oxygen
Products are light, water, oxidized flavin mononucleotide and long chain aliphatic carboxylic acid

66
Q

Tooth biofilms

A

Streptococcus mutans and Fusobacteria

67
Q

Consortia

A

Simple mixtures of taxa that collectively conduct biochemical reactions that convert a starting substance into one of applied or environmental importance
“biotransformations”

68
Q

k

A

Relationship between N and t

Specific growth rate constant

69
Q

k=

A

(logN2-logN1)2.303/(t2-t1)

in hrs^-1

70
Q

g

A

generation time

dependent on k

71
Q

g=

A

ln2/k

in hrs

72
Q

Balanced Growth

A

When oligotrophic microbes are supplied with unlimited food and permissive growth conditions, they grow and divide at maximum rates
All components of a population of cells and single cells increase proportionally

73
Q

What is used to measure RNA synthesis?

A

Radioactive uracil

74
Q

Submaximal growth rates

A

Restricted by nutrient availability or environmental conditions
Why microbes are present in most natural samples at lower densities

75
Q

Cell Yield

A

Absolute number of cells that can be produced

Determined by nutrient availability and the type of metabolism

76
Q

Cell Yield Copiotrophs

A

Directly related to the limiting nutrient available or type of metabolism
Cell yield is half when the amount of the limiting nutrient is halved

77
Q

Cell Yield Oligotrophs

A

Relationship with nutrient availability not clear
More restricted metabolisms
Lithoautotrophs seldom achieve cell densities greater than 10^6/mL

78
Q

Secondary metabolism

A

Unique metabolic processes during stationary phase

Ex: synthesis of antibiotics and pigments, use of alternate energy yielding and consuming pathways

79
Q

Richard Morita

A

Starvation induct stationary phase plays critical role in survival of microbes in the ocean

80
Q

Stress Resistance Response

A

Evolutionarily conserved
Hsp70 (DnaK) protein chaperone present in all bacteria and some Archaea
Widely distributed among eukaryotic microbes in mitochondria and chloroplasts

81
Q

Hsp70

A

Eukaryotes

82
Q

DnaK

A

Prokaryotes

83
Q

dnaK mutant

A

Only modestly sensitive to heat during growth but extremely sensitive during stationary
Protein refolding is critical

84
Q

Size and stationary phase

A

Cells become smaller
Differences are taxon-specific
Reductive division
Changes shape and increase surface are to volume ratio, increases ability to scavenge nutrients

85
Q

Viable but notculturable cells (VBNC)

A

Reversible, obscures the criteria for viability

Vibro cholera

86
Q

Rita R Colwell

A

VBNC vibrio cholera research

87
Q

How can viability be shown in VBNC cells?

A

Nutrient dependent increases in cell size

88
Q

Enterobacteria

A

VBNC, present in chlorinated drinking water and survive disinfection
Low level residuals must be maintained to maintain bacterial injury

89
Q

Maintenance energy

A

Energy consumed for cell maintenance
Transporting nutrients and waste products across envelope
Intracellular detoxification
Motility
Protein refolding
Becomes a large fraction in stationary phase
Energy storage compounds

90
Q

Stationary Genetics

A

Disable genes for DNA repair
Increase in spontaneous mutation
Mutators defective in mismatch repair pathway
Proteins naturally become depleted in stationary, elevates homologous recombination and mutation rate

91
Q

Layers of the Spore

A

Core, cortex, coat, exosporium

92
Q

Endospore coat

A

Comprised of multiple layers of specific proteins
Deposited in a particular order but not in synthesized order
Spore coat involved a process of auto assembly mediated by the proteins themselves

93
Q

Dipocolinic Acid

A

Diagnostic marker of endospores
Cortex
Overlapping mechanisms to confer thermal tolerance

94
Q

Core

A

Compressed version of a vegetative cell with DNA contained within a cytoplasmic space and a membrane

95
Q

Cortex

A

Surrounds the core and consists of peptidoglycan

96
Q

Protein Coat

A

Made up of multiple layers of spore specific proteins

97
Q

Exosporium

A

Surrounds the cortex and consists of a unique but thin layer of special protein

98
Q

Sporulation Stages

A

1: Vegetative cell
2: Septation and engulfment
3: Prespore protoplast formation
4: Cortex formation
5: Coat formation
6: Maturation
7: Spore release

99
Q

spo genes

A

Control sporulation
Mutations in any result in defective sporulation
spo mutants elucidated steps of sporulation

100
Q

Spo0A

A

key regulatory protein that initiates sporulation

phosphorylated or dephosphorylated

101
Q

Sporulation sigma factors

A

sigmaA: vegetative sigma
sigmaE: prepares parental cell, directs expression of genes specific to vegetative cell surrounding the endospore
sigmaF: prepares parental cell, directs gene specific to the endospore
sigmaG: activate genes necessary for terminal stages of endospore development
sigmaK: gene expression in the surrounding vegetative cell late in development

102
Q

sigmaF activates

A

sigmaG, activates genes for terminal endospore development

103
Q

sigmaE activates

A

sigmaK, activates genes for terminal development in the vegetative cell

104
Q

Biofilm Stages

A
  1. Transient attachment
  2. Permanent attachment
  3. Maturation
  4. Detachment
105
Q

EPS

A

extracellular polymeric substances
excreted slime layer
Channels and pores permeate during maturation, increase supply of oxygen and other nutrients
Provide structural integrity

106
Q

Transition to permanent attachment

A

Cell synthesizes EPS
OR
Production of specific proteins including pili, fimbriae, curli and adhesins that promote specific attachment

107
Q

Signal molecules biofilms

A

Homoserine lactones in proteobacteria

Peptides in Bacillus and Streptococcus

108
Q

Endocarditis

A

Infection of cardiac valve
Vegetation: bacterial cells combined with platelets and fibrin
Compromises blood flow and valve function
Recurrent source of infection
Cause of embolizatoin
Prolonged antibiotic therapy and removal of valve

109
Q

Cystic Fibrosis

A 
Congenital disease
Lung biofilms
Environment caused by mutations in CFTR promotes colonization and biofilm development
Pseudomonas aeruginosa
Death by asphyxiation
110
Q

Kidney Stones

A

15-20% accompany UTIs and derive from biofilms
Biofilm combine with struvite (magnesium phosphate and calcium apatite)
Forms when urease producing organisms create alkaline environment

111
Q

Biofilms and Evolution

A

Density is higher than planktonic
Increased rates of horizontal gene transfer
Evolution of pathogens

112
Q

Functions of Transport Systems

A
  1. Concentrative
  2. Discriminating
  3. Regulatory
  4. Versatile
113
Q

Importance of Transport Systems

A
  1. Efflux system
  2. Protectant uptake
  3. Environment sensing
  4. Catabolite repression
  5. Flagellar motor
  6. Ion regulation
  7. Proton translocation
  8. Nutrient acquisition
114
Q

Percentage of gene products that are transmembrane

A

18-20%

115
Q

Milton Saier

A

Transportation Classification System

116
Q

Channels/Pores Example

A

Glycerol permease

Glucose permease in Zymomonas mobilis

117
Q

Entner-Doudoroff Pathway

A

1 glucose > 2 ethanol + 2 CO2 + 1 ATP

Yields less ATP than normal glycolysis

118
Q

Primary Active Transport

A

F0F1 ATPase
Kdp system
Na+ transporting carboxylic acid decarboxylase

119
Q

Kdp system

A

Pumps K+ into the cell using ATP

120
Q

Na+ transporting carboxylic acid decarboxylase

A

Creates Na+ gradient to bring citrate into the cell
Uses energy from decarboxylation oxaloactetate to pump Na+ back out
citrate > oxaloacetate + acetate > pyruvate + CO2

121
Q

ABC systems

A 
ATP Binding Cassette
High substrate affinities
Substrate binding protein
Integral membrane spanning proteins
Inner membrane associated ATP hydrolysis proteins
122
Q

Ionophores

A

Dissipate ion gradients and inhibit secondary transport

123
Q

Osmotic Shock

A

Expose cells to in hypertonic buffer to EDTA

Removes divalent cations that hold together LPS

124
Q

How do anaerobes makes a pmf?

A

F0F1 ATPase

125
Q

How to measure transport and identify energy source?

A
  1. Radio-labeled substrates
  2. Control source of energy
  3. Use vesicles or proteoliposomes
  4. Mutational analysis
126
Q

Product:precursor exchange systems

A 
Oxalate > formate
Arginine > ornithine
Lactose > galactose
Citrate > lactate
Malate > Lactate (malate permease)
127
Q

Group Translocation

A

PEP dependent PTS

PEP > pyruvates phosphorylates Enz I which phosphorylates Hpr which phosphorylates Enz II which is substrate specific

128
Q

Hpr and Enz I

A

Cytoplasmic and not substrate specific

129
Q

Enz II

A 
Multiple domains
One integral (Enz IIC)
Substrate specific
130
Q

Hpr

A

Key intermediate phosphorylated at His15l

131
Q

Acid tolerance

A

HA is pumped in/out of the cell were it can dissociate

HA= acetic, propionic, benzoic acid

132
Q

Acid tolerance

A

Pump H+ out of cell
Pump malate in, convert to lactate using H+ and producing CO2, lactate leaves
Pump arginine in which creates ammonia, CO2, ornithine (pumped out)

133
Q

Osmotolerance

A

Betaine is pumped out or into the cell

134
Q

Cryotolerance in Saccharomyces

A

Trehalose permease symports trehalose with H+, can produce glucose as intermediate

Microbial Physiology (2 decks)

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