Exam 1 Flashcards
1
Q
Components of Prokaryotic Cell
A
Envelope, cytoplasm, nucleoid
2
Q
Components of Eukaryotic Cell
A
Chloroplast, cilium, endoplasmic reticulum, golgi, lysosome
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
4
Q
Eukaryotic Cell Size
A
10-100 um in length, 2-200 um in diameter
5
Q
Surface-to-volume ratio
A
3/r
6
Q
G+
A
Thick peptidoglycan layer
Teichoic and lipoteichoic acids provide stability
7
Q
G-
A
Lipopolysaccharide layer, thin peptidoglycan
8
Q
G- Cell Wall is made up of
A
Outer membrane, peptidoglycan layer
9
Q
G- periplasmic space
A
Between cell wall and inner plasma membrane
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)
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
12
Q
Cell Wall Functions
A
Determines cell shape, resists intracellular pressure
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
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
15
Q
Algal cell walls
A
Cellulose or pectin (polymer of galacturonic acid) or protein
16
Q
Mycoplasma, Thermoplasma cell wall
A
Lacks cell wall, require environment where external solute concentration is similar to intercellular
Avoid turgor pressure
17
Q
Bacterial and eukaryotic phospholipids
A
Use ester bond to couple glycerol and fatty acids
18
Q
Archaeal phospholipis
A
Use an ether bond to couple glycerol and fatty acids
19
Q
Hyperthermophilic archaea unique membrane
A
Lipid monolayer
20
Q
Outer membrane is found in _____ and result in the ______
A
Gram - and gram variable, periplasm
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)
22
Q
What is the behavioral consequence of the periplasm?
A
G- secrete less protein into the environment than G+
23
Q
Lipoprotein
A
Anchors outer membrane to the cell wall
Tail embedded in inner leaf of outer membrane
Protein component binds cell wall
24
Q
LPS
A
Endotoxin, elicits fever in humans
Made of Lipid A, core polysaccharide and O-polysaccharide
25
O-polysaccharide
made of hexoses in repeating clusters (glucose, galactose, rhamnose and mannose), varies significantly between strains of bacteria. Important distinguishing marker
26
Core polysaccharide
Varies in composition between organisms
27
Lipid A
Lipid portion of LPS, ester-linked FAs coupled to a disaccharide of N-acetyl glucosamine phosphate
28
Gram Variable
Acid fast
Mycobacteria
Made of phospholipid combined with mycolic acids, not LPS
Porins present
29
Mycolic acid
Long chain fatty acids extending 70 or more carbons
30
Small molecule transport mechanisms
Simple diffusion, osmosis, facilitated diffusion and active transport
31
Group Translocation is found in
Prokaryotes, chemically modifies incoming molecule consuming energy
32
What type of transport is only found in eukaryotes?
Pinocytosis and endocytosis
33
Cytoplasm
90% water
Highly reducing
Protein thiol groups remain protonated, minimizing sulfhydryl bonds
pH is constant, near neutral
34
Prokaryotic cytoplasm
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
35
What grows at pH
Archaea and possibly a few fungi
36
What grows at pH >10?
Bacteria and archaea
37
Eukaryotic cytoplasm
Complex
Contains nucleus and organelles
Facilitate movement of proteins and other molecules
Cytoskeleton
38
Cytoskeleton
Critical for cell division and movement
39
Crenarchaeal chromosomal organization
NAP (bacteria like)
40
Euryarchaeal chromosomal organization
Eukaryote like, histone proteins and nucleosomes
41
Primary transcript processing in Eukaryotes
Splice out introns, 5'-methylguanosine cap, 3' polyadenylate tail
42
Prokaryotic ribosomal subunits
30S + 50S = 70S
43
Eukaryotic ribosomal subunits
40S + 60S = 80S
44
Prokaryotic 30S subunit
16S rRNA
45
Prokaryotic 50S subunit
23S and 5S rRNA
46
Proteasome
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)
47
Storage Bodies
Polyhydroxybutyrate inclusions
Carboxyl connected to carbon chain, R group determines type > CH3 = PHB
Nitrogen rich compounds
Lipids
48
Capsules
```
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
```
49
Pilus
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
50
Flagellar Motor
Nanomachine
Rotate flagellum around axis
Made of Mot, Fli proteins, M and S rings, P and L rings
51
Flagellin
Protein subunits that make up flagellum
52
Bacterial vs Archaeal Flagella
Flagellin is similar among bacteria, but different in Archaea
Flagella evolved separately in the two groups
53
Flagellin is assembled at
The tip of the rod, not the base
| Flagellin monomers pass through the hollow core where they are assembled by cap proteins
54
Assembly of flagellum
Insertion of M and S rings, motor proteins, then P and L rings and finally the hook
55
Mot
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
Fli
Control direction of rotation, reversible depending on intracellular signals concerned with environmental conditions
57
Oligotrophy
Prefer conditions of limited nutrient availability
Do not exhibit unrestricted growth under nutrient excess conditions, divide at very slow rates
Open ocean
58
Copiotrophy
Exhibit unrestricted growth in response to conditions of nutrient excess
Model systems, achieve high densities in laboratory culture
59
Colony with diameter of 1 mm
10^8 cells (100 million)
60
Spectrophotometry can detect
Populations 10^7 cells or greater
61
Changes within a colony
Differences in oxygen, light availability, pH, nutrients and osmolarity
62
Death Phase
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
Quorum Sensing
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
Quorum sensing molecules
Homoserine lactones
| Small peptides
65
Flourescence
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
Tooth biofilms
Streptococcus mutans and Fusobacteria
67
Consortia
Simple mixtures of taxa that collectively conduct biochemical reactions that convert a starting substance into one of applied or environmental importance
"biotransformations"
68
k
Relationship between N and t
| Specific growth rate constant
69
k=
(logN2-logN1)2.303/(t2-t1)
| in hrs^-1
70
g
generation time
| dependent on k
71
g=
ln2/k
| in hrs
72
Balanced Growth
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
What is used to measure RNA synthesis?
Radioactive uracil
74
Submaximal growth rates
Restricted by nutrient availability or environmental conditions
Why microbes are present in most natural samples at lower densities
75
Cell Yield
Absolute number of cells that can be produced
| Determined by nutrient availability and the type of metabolism
76
Cell Yield Copiotrophs
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
Cell Yield Oligotrophs
Relationship with nutrient availability not clear
More restricted metabolisms
Lithoautotrophs seldom achieve cell densities greater than 10^6/mL
78
Secondary metabolism
Unique metabolic processes during stationary phase
| Ex: synthesis of antibiotics and pigments, use of alternate energy yielding and consuming pathways
79
Richard Morita
Starvation induct stationary phase plays critical role in survival of microbes in the ocean
80
Stress Resistance Response
Evolutionarily conserved
Hsp70 (DnaK) protein chaperone present in all bacteria and some Archaea
Widely distributed among eukaryotic microbes in mitochondria and chloroplasts
81
Hsp70
Eukaryotes
82
DnaK
Prokaryotes
83
dnaK mutant
Only modestly sensitive to heat during growth but extremely sensitive during stationary
Protein refolding is critical
84
Size and stationary phase
Cells become smaller
Differences are taxon-specific
Reductive division
Changes shape and increase surface are to volume ratio, increases ability to scavenge nutrients
85
Viable but notculturable cells (VBNC)
Reversible, obscures the criteria for viability
| Vibro cholera
86
Rita R Colwell
VBNC vibrio cholera research
87
How can viability be shown in VBNC cells?
Nutrient dependent increases in cell size
88
Enterobacteria
VBNC, present in chlorinated drinking water and survive disinfection
Low level residuals must be maintained to maintain bacterial injury
89
Maintenance energy
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
Stationary Genetics
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
Layers of the Spore
Core, cortex, coat, exosporium
92
Endospore coat
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
Dipocolinic Acid
Diagnostic marker of endospores
Cortex
Overlapping mechanisms to confer thermal tolerance
94
Core
Compressed version of a vegetative cell with DNA contained within a cytoplasmic space and a membrane
95
Cortex
Surrounds the core and consists of peptidoglycan
96
Protein Coat
Made up of multiple layers of spore specific proteins
97
Exosporium
Surrounds the cortex and consists of a unique but thin layer of special protein
98
Sporulation Stages
1: Vegetative cell
2: Septation and engulfment
3: Prespore protoplast formation
4: Cortex formation
5: Coat formation
6: Maturation
7: Spore release
99
spo genes
Control sporulation
Mutations in any result in defective sporulation
spo mutants elucidated steps of sporulation
100
Spo0A
key regulatory protein that initiates sporulation
| phosphorylated or dephosphorylated
101
Sporulation sigma factors
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
sigmaF activates
sigmaG, activates genes for terminal endospore development
103
sigmaE activates
sigmaK, activates genes for terminal development in the vegetative cell
104
Biofilm Stages
1. Transient attachment
2. Permanent attachment
3. Maturation
4. Detachment
105
EPS
extracellular polymeric substances
excreted slime layer
Channels and pores permeate during maturation, increase supply of oxygen and other nutrients
Provide structural integrity
106
Transition to permanent attachment
Cell synthesizes EPS
OR
Production of specific proteins including pili, fimbriae, curli and adhesins that promote specific attachment
107
Signal molecules biofilms
Homoserine lactones in proteobacteria
| Peptides in Bacillus and Streptococcus
108
Endocarditis
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
Cystic Fibrosis
```
Congenital disease
Lung biofilms
Environment caused by mutations in CFTR promotes colonization and biofilm development
Pseudomonas aeruginosa
Death by asphyxiation
```
110
Kidney Stones
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
Biofilms and Evolution
Density is higher than planktonic
Increased rates of horizontal gene transfer
Evolution of pathogens
112
Functions of Transport Systems
1. Concentrative
2. Discriminating
3. Regulatory
4. Versatile
113
Importance of Transport Systems
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
Percentage of gene products that are transmembrane
18-20%
115
Milton Saier
Transportation Classification System
116
Channels/Pores Example
Glycerol permease
| Glucose permease in Zymomonas mobilis
117
Entner-Doudoroff Pathway
1 glucose > 2 ethanol + 2 CO2 + 1 ATP
| Yields less ATP than normal glycolysis
118
Primary Active Transport
F0F1 ATPase
Kdp system
Na+ transporting carboxylic acid decarboxylase
119
Kdp system
Pumps K+ into the cell using ATP
120
Na+ transporting carboxylic acid decarboxylase
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
ABC systems
```
ATP Binding Cassette
High substrate affinities
Substrate binding protein
Integral membrane spanning proteins
Inner membrane associated ATP hydrolysis proteins
```
122
Ionophores
Dissipate ion gradients and inhibit secondary transport
123
Osmotic Shock
Expose cells to in hypertonic buffer to EDTA
| Removes divalent cations that hold together LPS
124
How do anaerobes makes a pmf?
F0F1 ATPase
125
How to measure transport and identify energy source?
1. Radio-labeled substrates
2. Control source of energy
3. Use vesicles or proteoliposomes
4. Mutational analysis
126
Product:precursor exchange systems
```
Oxalate > formate
Arginine > ornithine
Lactose > galactose
Citrate > lactate
Malate > Lactate (malate permease)
```
127
Group Translocation
PEP dependent PTS
| PEP > pyruvates phosphorylates Enz I which phosphorylates Hpr which phosphorylates Enz II which is substrate specific
128
Hpr and Enz I
Cytoplasmic and not substrate specific
129
Enz II
```
Multiple domains
One integral (Enz IIC)
Substrate specific
```
130
Hpr
Key intermediate phosphorylated at His15l
131
Acid tolerance
HA is pumped in/out of the cell were it can dissociate
| HA= acetic, propionic, benzoic acid
132
Acid tolerance
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
Osmotolerance
Betaine is pumped out or into the cell
134
Cryotolerance in Saccharomyces
Trehalose permease symports trehalose with H+, can produce glucose as intermediate
