Exam (after Midterm 1 Content) Flashcards
(304 cards)
1
Q
What was the purpose of the Griffith Experiment and how was it performed
A
Evidence that DNA may be the hereditary material
When killed smooth and live rough streptococcus pneumoniae were separately added to separate mice, they both lived
Live smooth killed the mouse
When killed smooth and live rough we’re added together, the mouse died
Rough cells converted to smooth
2
Q
Avery, MacLeod, and McCarty experiment: steps and purpose
A
Purpose: is DNA, RNA, or protein the causative agent of transformation
Heat killed smooth strain was treated with enzymes that killed proteins, DNA or RNA, and then were incubated with living rough cells
Rough cells do not grow on agar
All plates showed growth except one treated with DNase
DNA is the transforming principle
3
Q
Packaging of DNA in the 3 domains
A
Bacteria: singular circular chromosome, supercooled
Archaea: singular circular chromosome, histones
Eukarya: multiple linear chromosomes, histones
4
Q
Replication initiation in E. coli
A
DnaA molecules interact with the oriC bp repeats forming a complex, DNA is unwound
DnaC delivers the DnaB helicase to the replication complex
Single stranded binding proteins present
5
Q
Initiation of DNA replication in eukaryotes
A
Multiple origins of replication on each chromosome
Origin replication complex (orc) binds Automatically replicating sequence (ARS)
Proteins such as Cdt1, Cdc6 and MCM are recruited
DNA is unwound and SSB proteins keep strands apart
6
Q
Replication elongation in bacteria
A
DNA polymerase III adds nucleotides to RNA primers that are synthesized by RNA primase
Continuous and discontinuous strands (leading and lagging)
Clamp keeps DNA polymerase III bound to DNA
RNA primers removed and replaced with DNA by DNA polymerase I which has 5’ to 3’ exonuclease activity
Sealed by DNA ligase
7
Q
Clamp processivity factor
A
Found in all 3 domains
Beta clamp in E. coli
8
Q
Circular Replication termination
A
Tus proteins interact with DnaB to open DNA then they bind ter sites stopping elongation
Topoisomerase is recruiter
Chromosomes disentangled
9
Q
Linear replication termination
A
RNA primer removed, produces 5’ end that cannot be extended by DNAP
telomerase binds and extends the 3’ end using an RNA template
10
Q
Meselson and Stahl
A
Add N15 labelled cells to N14 medium and grow for 4 gen
Results consistent with semi conservative replication
Generation 2 had one N15 and one N14 strand
11
Q
Approximate length of mRNA
A
500-10,000 nt
12
Q
Typical gene size of bacteria
A
1 kb
13
Q
mRNA can be _______________, meaning it encodes several proteins
A
Polycistronic
14
Q
Do bacterial genes contain introns
A
No
15
Q
Length of tRNA
A
75-100 nt
16
Q
tRNA orientation
A
3’ to 5’
17
Q
rRNA size
A
1500 to 1900 nt for small subunit
2900 to 4700 nt for large subunit
18
Q
Eukaryotic ribosome subunit size
A
Small 40S
Large 60S
Total 80S
19
Q
Bacteria ribosome subunit size
A
Small 30S
Large 50S
Total 70S
20
Q
Small subunit rRNA in eukaryotes
A
18S
21
Q
Small subunit rRNA in prokaryotes
A
16S
22
Q
Which has more rRNA? Pro or eukaryotes
A
Eukaryotes
23
Q
More proteins or rRNA in the ribosome?
A
Proteins
24
Q
————- factors bind bacterial promoters to allow RNAP to recognize them
A
Sigma
25
Positions of consensus regions in E. coli
-10 and -35
26
What is the main sigma factor in E. coli
RpoD
27
Transcription initiation elements in eukaryotes bound by transcription factors
Octamer box
CAAT box
GC box
TATA box (-20)
28
Different sigma factors in bacteria can_______________________
Direct RNAP to different sets of genes that are co-regulated
29
How many RNA polymerase in bacteria
1
30
How many RNA polymerase in eukaryotes
3
31
This protein interacts with the TATA box
TATA Binding protein (TBP)
32
What is TFIIB
A transcription factor in eukaryotes which binds the promoter
33
Transcription initiation in archaea is similar to _______ in regard to transcription factors and similar to ______ in regard to RNAP
Eukaryotes , bacteria
34
Transcription termination in bacteria can be done by the _____ protein or through ________
Rho
| Rho-independent termination
35
Rho independent termination involves a _______ rich in _________ followed by a ____ rich sequence
A hairpin structure
GC
Uracil
36
What is the function of the uracil rich sequence in Rho independent termination
Has less H bonds so is easier to separate
37
3 pots transcriptional modifications in eukaryotes
5’ 7-methyl guanosine cap
3’ polyA tail
Intron splicing
38
Which enzyme adds amino acids to tRNA
aminoacyl tRNA synthetase
39
Which nucleotide is responsible for the wobble effect
3rd in codon
| 1st in anticodon
40
Which amino acid charges tRNA that initiates translation of AUG in bacteria
N-formyl methionine
41
Amino acids are added to the __ end of the tRNA
3’
42
The shine delgarno sequence is
A sequence complementary to the 16S sequence in bacteria
| Interacts with 16S in ribosome to initiate translation
43
In eukaryotes mRNA is bound by ___________ and one binds the ________
Several polypeptides
| 5’ cap
44
Eukaryal mRNA is _______
Monocistronic
45
Charged tRNAs enter the _____ site
A
46
Termination of translation
Release factors when stop codon is reached
47
_______ help proteins fold
Chaperones
48
Protein modifications in eukaryotes include
Phosphorylation
Acetylation
Methylation
Glycosylation
49
______________ direct proteins to appropriate locations
Signal peptides
| Short AA sequences at N terminus
50
How many genes in human cells that encode proteins
Approx 22,000
51
When does regulation of gene expression occur
During transcription
Translation
Post translation
52
Composition of lactose
Galactose and glucose
| Linked by beta 1,4
53
Function of beta galactosidase
Cleaves beta 1,4 linkage in lactose
54
Substrate for the detection of beta galactosidase
ONPG
55
Lactose permease function
Transports lactose into cell across cell membrane
56
When e.coli are grown with glucose and lactose, which is consumed first
Glucose
57
Lac Operon not expressed until
All glucose is used up
58
LacI function
Codes for lacI repressor which binds the operator inhibiting transcription
59
CAP site function
Activator binding site
| DNA site bound by activator
60
Promoter function in lac operon
Bound by RNAP to direct initiation of transcription
61
LacO function
Operator
| Bound by repressor
62
Effector function lac Operon
Binds activator or repressor proteins to modify gene activity
63
Inducer function
Increases transcription levels by enabling activator or disabling repressor
64
Corepressor
Decreases transcription by binding repressor
65
LacZ codes for
Beta galactosidase
66
LacY codes for
Lactose permease
67
When is lacI transcribed
Always
| At a low basal level
68
What recognizes the allosteric site on the laci repressor
Allolactose
69
The trp operon encodes for
Proteins in the tryptophan synthesis pathway
70
When trp is not present
It cannot bind the trp repressor, so it cannot bind the operator
Transcription continues
71
When trp is present
It binds the repressor so it can bind the operon
| No transcription
72
When glucose levels are high and cAMP levels are low
cAMP cannot bind the CRP activator
| RNAP has a low affinity for the promoter and will not bind
73
When glucose levels are low and cAMP levels are high
cAMP bind CRP
| The CRP-cAMP complex binds the activator binding site increasing RNAP affinity for the promoter
74
Sigma 70 (RpoD) function
Housekeeping
75
Sigma 32 (RpoH) function
Heat shock
76
Sigma 54 (RpoN) function
Nitrogen starvation
77
Sigma-38 (RpoS) function
Stress
78
Purpose of SOS response in bacteria
Allows cells to recognize and respond to serious DNA damage
79
SOS response experiment with E. coli
Bacteria exposed to UV light and infected with damaged phages repaired these phage but they had high rates of mutation (more phage, more mutations)
Bacteria that were not exposed to UV and that were infected with damaged phages could not repair them as efficiently and lower mutation rates (few phage, few mutations)
80
lexA function
DNA binding transcriptional repressor of the SOS genes
| Binds the operator and shuts of transcription
81
recA function
Recombination and regulation of the SOS response, binds ssDNA
Becomes a protease which cleaves lexA so the genes can be expressed
82
SOS regulon no DNA damage
LexA keeps SOS regulon genes repressed
| RecA is inactive
83
SOS regulon DNA damage
RecA cleaves the LexA repressor
| SOS genes expressed
84
Quorum sensing definition
Chemical signalling system that controls gene expression
85
What is the function of autoinducers
Cells release them into the environment and as the population density increases in an area the concentration of autoinducer does too
Detecting changes in autoinducer levels causes regulation of gene expression
86
The lux quorum sensing system is found in this bacteria
Vibrio fischeri
87
Where do Vibrio fischeri live in
Hawaiian bobtail squid
88
When do Vibrio fischeri emit light and what enzyme do they use
When in the light organ of the squid
| Luciferase
89
What is the autoinducer made by Vibrio fischeri
AHL
90
This activator interacts with AHL when it reaches a high concentration
LuxR
91
The AHL LuxR complex binds the _________ for activation
Lux box
92
At high AHL concentration
AHL and LuxR interact and transcription is activated transcribing luxA and luxB which are needed for luciferase production
93
At low AHL levels
AHL and LuxR do not interact
Lux box is not bound for activation of transcription
Light and luciferase is not produced
94
Mechanisms controlled by quorum sensing
Motility
Conjugation
Biofilm formation
Pathogenesis
95
Components of the two component regulatory system
A sensor kinase and a response regulator
96
Sensor kinase function
Often a histidine protein kinase (HPK)
Located in plasma membrane
Detect environmental stimulus
97
Response regulator function
Inside the cytoplasm
| Regulate transcription
98
Two component regulatory system in Agrobacterium tumefaciens
Genes expressed under similar conditions to plant wound
virA is an HPK protein which interacts with sugars and phenolic compounds at low pH
virG is an activator RR protein for other vir genes
99
Regulatory RNAs
Small non coding RNA that control gene expression at transcriptional or translational levels
100
General attenuation mechanism
If the ribosome quickly follows RNAP, a terminator hairpin will form in the leader sequence and RNAP detaches
Stalling out of the ribosome on the leader sequence allows transcription to continue
101
Can attenuation occur in eukaryotes? Why or why not?
No, because transcription and translation occur separately
102
High levels of tryptophan: attenuation
Terminator loop forms (regions 3 and 4) and stops transcription, tryptophan not made
Ribosome stops at stop codon
103
Low levels of tryptophan: attenuation
Terminator loops does not form and transcription continues
Tryptophan made
Ribosome stops at trp codons
Region 2 anneals to 3
104
Where in bacterial mRNA are riboswitches found
The 5’ UTR
105
Riboswitch function
Acts as a binding site for ligands which influence downstream structure regulating transcription and or translation
Transcriptional: terminator loop
Translational: ribosome binding site
106
Intrinsic factors that effect food spoilage
```
Water activity
Osmolarity
Nutrient content
pH
Antimicrobial constituents
Biological structures
```
107
Extrinsic factors that effect food spoilage
Temperature
Humidity
Gases
108
Adding solutes to water ———- it’s water activity
Decreases
109
Bacterial pathogens cannot grow at a water activity _______ and yeasts and moulds ________
<0.86
| <0.65
110
Reducing water activity by:
```
Drying
Adding solutes (sugar or salt)
```
111
Most microorganisms require a water activity greater than
0.99
112
Canning process
Heating food to 100 degrees for extended period under pressure
113
Pasteurization process
Heating liquids to 63 degrees Celsius for minimum 30 min
| Kills 99% of organisms
114
Pickling process
Using acid (vinegar)
115
Modified atmosphere packaging
Vacuum seal
| Change atmosphere to inhibit microbial respiration (oxygen depletion)
116
Chemical preservatives
Lower pH
| Interfere with cellular respiration
117
Irradiation for food preservation
Ionizing radiation causes oxidative damage and toxic free radical production
UV radiation causes thymine dimers
118
Hurdle technology
Apply multiple constraints to more effectively preserve food
| Ex temp, ph, aw, etc.
119
Clostridium botulinum
Gram positive
Obligate anaerobe
Produces botulism neurotoxin (most potent neurotoxin known)
Associated with improperly canned food
120
How to control botulism
Pickling, pH less than 4.6
Salt curing, aw less than 0.96
High oxygen
Temp less than 4.4 deg
121
What was the bacteria responsible for the Romaine lettuce infection outbreak?
E.coli O157:H7
122
What toxin was responsible for the Romain lettuce infection and what is its function
Shiga toxin
| Inhibits protein synthesis in target cells
123
How did E.coli O157:H7 acquire the shiga toxin gene
Horizontal gene transfer from a prophage
124
Which bacteria was responsible for the listeria outbreak of 2008
Listeria monocytogenes
| Gram positive firmicute
125
Why can listeria monocytogenes evade control in human foodstuffs
Can grow at temperatures as low as 0 deg C
Can move within eukaryotic cells by polymerization of actin
Facultative anaerobe (can grow with or without oxygen)
126
Which bacteria is one of the most common causes of food poisoning
Camplyobacter jejuni
Gram negative bacteria
Spiral shaped
127
Which bacteria grows best in aerobic environments but can also grow anaerobically, and causes food poisoning
Staphylococcus aureus
128
Lactic acid bacteria characteristics
Gram positive
Ferment glucose to lactic acid
Grow anaerobically but can grow with oxygen
Lack catalase (have alternative enzymes)
129
Lactic acid bacteria must grow in:
Environment where sugars are present
| Complex media that fulfills nutrition requirements
130
Some LAB cause disease, most notably members of the genus ________
Streptococcus
131
Why are LAB so important for food fermentation
Taste and texture
| Inhibit food spoilage by producing lactic acid and growth inhibiting substances
132
Preparation of yogurt involves:
Pasteurization, adding starter cultures, and fermentation
133
What is the purpose of starter culture in food
Helps control fermentation
| Produces acid lowering pH and preventing spoilage
134
_________ is used in koji fermentation to produce products like soy sauce
Mold
| Koji is the starter culture for various molds
135
Kombucha starter culture
SCOBY
| Starter culture of yeast and bacteria
136
How to make mash for beer
Barley malt added to warm water, enzymes activated, and starch is broken down by amylase to maltose creating wort
137
Boiling step of beer making
Boiling kills unwanted microbes
| Hops are added to add flavour and act as an antibacterial
138
Beer fermentation
Wort is cooled and yeast is added
| Maltose is converted to ethanol and co2 which carbonates beer
139
How is vinegar produced
Acetic acid bacteria metabolize ethanol to acetic acid
| Ethanol sprayed on wood chips with a biofilm of bacteria
140
Which bacteria are used to make vinegar
Gluconobacter and acetobacter
141
Foodborne intoxication
Microbial toxins in food, symptoms appear quickly
142
Foodborne infection
Contaminating microbes in food, delay in symptoms (after growth)
143
Goals for treating wastewater sewage
Remove total organic carbon
Remove harmful organisms
Reduce inorganic compounds
Reduce persistent organic pollutants
144
Wastewater treatment steps
Pre treatment: remove large objects
Primary treatment: remove sediments and grease
Secondary treatment: uses activated sludge (aerobic), microbes to break down organic compounds
Tertiary treatment: filtration of nitrogen and phosphates
Disinfection: chlorination, UV, ozonation
145
Drinking water purification steps
```
Screening
Flocculation
Sedimentation
Sludge treatment
Filtration
Disinfection
Storage
```
146
The casein milk protein family contains ________ and _________ at pH 4.6
Phosphorous
| Precipitates
147
The serum whey proteins do not contain ________ and _________ at pH 4.6
Phosphorous
| Does not Precipitate
148
Which protein family provide a good source of calcium for milk consumers
Casein
149
Carbon cycle in plants, algae and photosynthetic bacteria
CO2 to C6H12O6
150
Carbon cycles in eukaryotes, bacteria and archaea
C6H12O6 to CO2
| Decomposition
151
Carbon cycle in methanogens
C6H12O6 to CH4
152
Carbon cycle in methanotrophs
CH4 to C6H12O6
153
The carbon cycle summary
Incorporation of carbon from the atmosphere into biomass and release of carbon into the atmosphere through decomposition of biomass
Photosynthesis and respiration
154
Methanogenesis
Metabolism of organic matter or CO2 to methane under anaerobic conditions
155
Methanogens rely on ______ to produce __________ for methanogenesis
Other organisms
| Simple organic substrates
156
Methanogens form __________ with other organisms
Syntrophic relationships
157
What sources produce methane
```
Termites
Wetlands
Landfills
Rice cultivation
Domestic animals
Fossil fuels
Oceans
```
158
Type I methanotrophs utilize the ____________ pathway
RuMP
159
Type II methanotrophs utilize the _________ pathway
Serine
160
Are methanotrophs aerobic or anaerobic
Can be both
161
Which pathway do aerobic methanotrophs use
Either the RuMP or serine
162
Which enzyme do aerobic methanotrophs use to oxidize methane
Methane monooxygenase MMO
163
What process converts biologically inaccessible N2 to accessible NH3
Nitrogen fixation
164
Nitrogen fixation is generally under ____ conditions but can be under _____
Aerobic
| Anaerobic
165
Ammonia is used to:
Make amino acids or by lithotrophs as energy
166
Denitrification
Removes nitrate and converts it to nitrogen gas
167
As nitrogen is converted from nitrate to ammonia, it’s oxidation state:
Decreases
168
Which enzyme reduces N2 to ammonia
Nitrogenase
| Very sensitive to oxygen
169
Nitrification
Oxidation of NH3 to nitrite to nitrate
170
Nitrifying bacteria are:
Chemolithoautotrophs
171
Ammonia oxidizers harvest energy from oxidation of ammonia using
AMO and hydroxylamine oxidoreductase
172
Nitrifiers _______ from the oxidation of nitrite to nitrate using ______
```
Harvest electrons
Nitrite reductase (NOR)
```
173
Which process accounts for 50% of loss of nitrogen from marine environments
Denitrification
174
Bacteria and archaea use ___ and ____ as terminal electron acceptors in anoxygenic environments
Nitrogen and sulfur compounds
175
Chemical fertilization through the _____________ has nearly doubled flux of reactive nitrogen into the environment
Haber-Bosch
176
Ecosystem
Interactions and exchange of materials between organisms and their environment
177
Success of microbes in a niche depends on
Their ability to obtain nutrients and produce biomass
178
Formation of a biofilm
Adhesion by a primary colonizer
Cells divide
Microcolony produces EPS
Introduction of secondary colonizers
179
EPS/slime function in a biofilm
Protects biofilm
| Forms water filled channels for transport of nutrients and wastes
180
What percentage of microbes can be cultured in a laboratory
0.1%
181
Enrichment cultures
Promote growth if desired microbes over undesired cells
182
Winogradsky column
lake sediment in a cylinder
Carbon and sulfur added
Placed in sunlight
Creates layers of different microorganisms
183
Direct sequencing
Extract DNA from environmental sample
PCR using universal primers for rRNA and sequencing
Compare to known databases
184
Fluorescent in situ hybridization
Labeled oligonucleotide probes bind specific RNA or DNA in a mixed population of cells
Visualized under microscope
185
Metagenome library
DNA from an environmental sample used to construct a genome library
186
Primary producers
Capture light through photosynthesis
| Inorganic carbon to organic carbon
187
Consumers
Heterotrophs that ingest organic carbon molecules
188
How much of the marine biomass is made up of microbes
Over 98%
189
These microbes are often present in marine environments
Oligotrophs
| Low levels of nutrients including N,P, Fe
190
Nutrient influx effects
Farmland runoff adds N and P to the water
Phytoplankton proliferate
Heterotrophic microbes feed on phytoplankton and consume too much oxygen
Heterotrophs die due to low oxygen levels
191
Coastal dead zones
Hypoxic
| N and P stimulate growth of algae and Cyanobacteria and upon their death heterotrophic organisms use all of the oxygen
192
How to enrich for nitrogen fixing bacteria
Medium without nitrogen containing organic material
| Can use nitrogen gas from air to convert to usable molecules
193
Photosynthetic microbes in the ocean produce how much of the atmospheres oxygen
1/3
194
Surface photic zone
Penetrated by light
Populated by photosynthetic phytoplankton And Cyanobacteria
Non photosynthetic zooplankton
Pelagibacter (SAR11) present in very high quantities
195
Pelagibacter
Small genome, energetically efficient
| Highly specified for the environment, little junk DNA
196
Dark mid water zone
Fed by organic matter produced in upper surface water
197
Deep sea zone
Barophiles and pliezophiles which withstand high pressure
198
Dilution to extinction method
Inoculate very dilute sea water into autoclaved sea water followed by incubation
25-30% of cells were SAR11 proteobacteria
199
Proteorhodopsin
Light driven proton pump
Genes that encode for it are present in SAR11
Many sequences found in aquatic sample similar to proteorhodopsin
200
What nutrients are often limiting in the ocean
Fe and P
201
How do soils form
Microbial decomposition of plant and animal matter combines with abiotic minerals and nutrients excreted from plant roots
202
Rhizosphere
Area around the plant root
| Supports growth of microbes
203
Can life exist in the absence of photosynthesis driven primary production?
Yes
| Nutrients can be carried from primary producers to areas where sunlight cannot reach
204
Microbes in harsh, deep surface environments depend on ___________ for production of organic compounds
Chemolithoautotrophy
205
454 sequencing
DNA or RNA sheared into small fragments
Adapter sequences ligated to the fragments which each anneal to one bead
Fragments amplified by PCR and each bead is placed in the well of a slide containing DNA sequencing reagents
Each of the 4 dNTPs is added sequentially to the wells sequencing the fragments through fluorescence
Based on pyrosequencing
206
Illumine sequencing
4 Fluorescently labelled nucleotides and terminator added one cycle at a time to a slide
Terminator and previous base removed after each cycle
207
Nanopore sequencing
Guides ssDNA through protein pore that reads bases as they exit
Reads longer sequences than illumina
208
PacBio sequencing
High accuracy and longer sequences
| Can explore epigenetics
209
Horizontal gene transfer
Movement of DNA between organisms rather than from parent to offspring
Can be found by comparing GC content of organisms
210
Proteomics
Separate proteins on a gel
Split proteins into smaller peptides and determine molecular weight using mass spec
BLAST to sequence
211
Symbiont definition
An organism that has entered a long-standing and intimate relationship with an organism of another species
212
Syntrophy
Provision of nutrients from a microbes that the organism is unable to synthesis themselves
213
In syntrophic relationships, both partners depend on each other for:
Energetic reasons
| Perform a fermentation process neither could run on their own
214
Ectosymbionts
Live on the surface of their host
215
Endosymbionts
Live within the body or cells of a host
216
_______ and __________ live on the human skin and play a role in immunity
Firmicutes and actinobacteria
217
What is the most enriched part of the human body with anaerobic bacteria
The intestinal tract
218
What is the order of microbes in the small intestine (10^?)
10^10
219
How do herbivorous vertebrates break down cellulose from food
Depend on their symbiotic microbes for most of their caloric intake
Don’t posses enzymes to break down cellulose
220
Humans are __________ fermenters, where the primary site of fermentation is in the _______
Colonic
| large intestine
221
Cecal fermenters: definition and examples
Enlarged cecum that acts as primary fermentation site for breakdown of plant tissue
Rabbits, mice, herbivorous birds
222
Rumen fermenters: definition and examples
Evolved a specialized organ (the rumen) as the primary site of microbial fermentation
Deer, cattle, sheep
223
Primary endosymbionts of insects show evidence of:
Co-speciation
224
Primary endosymbionts of invertebrates are found exclusively in:
Specialized host cells called bacteriocytes which are transmitted from mother to offspring
Can be required for survival or fertility
225
Secondary endosymbionts live:
Can live outside of the host and aren’t restricted to specialized cells
Not always present or maternally transmitted
226
Example of primary and secondary symbionts of invertebrates
Primary: Buchneria with sap-feeding aphids
Secondary: Wolbachia can colonize many insect species, can reduce dengue virus spread in mosquitos
227
What is lichen composed of and what is the role of each component
Fungi (mycobiont) and and a photosynthetic microbe (photobiont, which can be Cyanobacteria or algae) in a symbiotic relationship
Photobiont performs photosynthesis and supplies C and N
The mycobiont provides inorganic nutrients and a protected environment
228
~85% of plant families participate in symbiosis with:
Mycorrhizal fungi which colonize roots
Roots provide fixed carbon, and fungus aids in nutrient acquisition from soil by penetrating the plant cell wall with its hyphae
229
What is the only way nitrogen can enter the biosphere
Nitrogen fixation by bacteria or archaea
230
What is the nitrogen fixing bacteria that forms a symbiotic relationship with legumes
Rhizobium
Legume forms a root nodule for the bacteria and they fix and provide nitrogen to the plant
Legume provides fixed carbon
231
What protects the oxygen sensitive nitrogenase in rhizobium
The root nodule and leghemoglobin of the legume plant which tightly binds oxygen
232
How do rhizobia infect the legume
Attach to the root hair, formation of a Shepards crook and an infection thread
233
Infectious disease definition
Disease caused by a microbe that can be transmitted from host to host
234
Zoonotic disease definition
Infectious disease in animals that can cause diseases when transmitted to humans
Ex. Rabies
235
Pathogen definition
Microbes that can cause disease
236
Primary pathogen
Produce disease readily in healthy hosts
237
Opportunistic pathogens
Only cause disease when displaced to an unusual site or when host has weakened immune system
238
Exotoxin
Secreted proteins that negatively affect the host cells
239
Endotoxins
Part of the microbial structure itself
240
Do viruses produce toxins?
Typically no, replication typically induces cell death via immune responses to viral spread
241
What is the purpose of mucus in the inner surfaces of the body
Sticky layer that traps microbes, which is then swept out by cilia
242
Innate immune response
All multicellular eukaryotes
Immediate and nonspecific immune response
Inflammatory response recognizes PAMPs which are detected by TLRs
243
TLR 1 and 2
Recognize lipoteichoic acids
244
TLR 2 and 6
Recognize lipopeptides
245
TLR 4
Recognize LPS
246
TLR 5
Recognize Flagellin
247
TLR 10
Ligand unknown
248
Adaptive immune response
In vertebrates
A specific immune response
B cells and T cells coordinate to recognize and remember specific antigens
249
Three steps for a microbe to cause disease
Gain access to host tissues
Overcome host defences
Obtain nutrients from host
250
Virulence factors purpose
Help the pathogen gain access to the host tissues, evade host defences, and access limiting nutrients
251
What is fibronectin
A large glycoprotein found in plasma and in extracellular matrix
Prime target for pathogen binding
252
How does gonorrhoea attach and invade host cells
Uses fimbriae to attach
Endocytosis and exocytosis
Replication and spread of infection
253
Fimbriae
Specialized pili used for attachment
Binds to receptor on host cell
Can be altered to evade immunity
254
Special adherence proteins
E.coli can engineer attachment with virulence factors Tir and Intimin protein
Tir is made by bacteria and excreted through the type III secretion system
Intimin produced by bacteria and interacts with Tir to act as a landing pad for bacterial cell
255
What microbe causes gastric ulcers
Helicobacter pylori
256
Effect of LPS on mammals
An endotoxin
Toxic to mammals, released upon bacterial death triggering inflammation
Can lead to septic shock or death
257
What can act as an endotoxin in gram positive bacteria
Lipoteichoic acids
258
Components of LPS
Lipid A: toxic activity
Core polysaccharide
O-antigen
259
AB toxin structure
A subunit has toxic enzymatic activity
| B subunit binds the cell receptor
260
Diphtheria, pertussis, and cholera toxins work by ______
ADP ribosylation of target molecules (EF2 and Cyclase)
261
Function of shiga toxins
Cleaves rRNA preventing ribosome synthesis
262
Function of botulism and tetanus toxins
Inactivate motor neuron proteins involved in activation of halting of muscle contraction
Results in paralysis
263
Cytolysins
Toxins that act on the plasma membrane to encourage cell lysis to provide nutrients for pathogens
264
Hemolysins
Cytolysins that target and lyse red blood cells to get iron from host
265
alpha toxin and listerolysin are:
Pore forming cytolysins
| Cause apoptosis and membrane disruption
266
Lecithinases are:
Membrane degrading cytolysins
267
How does an egg yolk plate work
The egg yolk contains lipids that when degraded produce a precipitate
268
Superantigen function
Act on helper T cells, over activating them and causing a systemic inflammatory response which does not efficiently target the pathogen
269
The type III secretion system is similar to _______
Flagella
270
Type IV secretion system is similar to ________________
Bacterial conjugation machinery
| Spans inner and outer membrane and injects effectors into host
271
_______ systems are associated with pathogenesis
Type III and IV secretion
272
Capsules as virulence factors
Extracellular polysaccharide matrix used to evade the host immune response and hide from receptors on immune cells
Can also play a role in attachment
273
Siderophores
Iron binding molecules that compete with host iron binding proteins
274
Mechanisms to obtain iron from host cells for pathogens
Siderophores
Bacterial transport proteins
Lower pH
Hemolysin
275
How do bacteria become pathogens
Horizontal gene transfer
| Uptake of DNA from the environment, conjugation, transformation
276
Pathogenicity islands
Can encode various virulence factors
Usually have low GC content
Flanked by repeat units and enzymes for movement
Often adjacent to tRNA genes
277
Lysogenic phages can _____________ by transduction and incorporation into genome
Transfer pathogenicity genes to bacteria
278
What is the natural role of restriction enzymes in bacteria
To protect against viruses
| Will cleave unmethylated phage DNA while methylated bacterial DNA is protected
279
CRISPR cas function
CRISPR locus is transcribed forming crRNA
Cas genes expressed to form cas proteins
CRISPR cas complex surveys cells for complementary phage DNA targeting the DNA for destruction
280
What are the 2 main uses of microbes in the pharmaceutical industry
Produce secondary metabolites with therapeutic properties
| Hosts for production of human proteins
281
What was the best selling pharmaceutical in history
Atorvastatin
282
Antibiotics interfere with
```
Peptidoglycan synthesis
Membrane integrity
DNA synthesis
Transcription
Folic acid synthesis
Ribosome function
```
283
Basic principle of industrial fermentation
Convert low cost biomass to high value products that are used in medicine and proteins
284
Primary metabolite
Product of metabolic process associated with growth
| Ex. Fermentation byproducts such as alcohol
285
Secondary metabolites
Non-growth associated metabolic product, often in stationary phase
Ex. Antibiotics
286
Systems used for industrial fermentation
Fed-batch reactors
| Chemostat
287
How can molecular biology tools be used to improve microbial strains
Random mutagenesis by chemical/radiation exposure followed by screening for mutations
The best antibiotic producers are kept
Drawbacks: possibility of negative mutations, screening can be difficult
288
Conditions for penicillin production
Aerobic
Various carbon sources
Sterile
Extracted with acetate
289
Original penicillin strain used __________ yielded 1mg/L, and now ___________ yields 50g/L
Penicillium notatum
| Penicillium chrysogenum
290
How are bacteria used to express desired proteins for pharmaceuticals
An expression plasmid for the production of the a tagged fusion protein is transformed into the bacteria to be expressed, the cells are lysed and the lysate is purified
291
Arnold’s discovery of directed enzyme evolution
Start with an enzyme with similar properties to the desired ones
Introduce random mutations into the genes and insert them into bacteria to express mutant enzymes
New enzymes are tested and most effective are selected
New mutations introduced and cycle is repeated
292
Why are microbial enzymes favoured over chemical synthesis
They produce stereospecific reactions
293
Biotechnology definition
Use of biological processes or organisms for the production of goods or services
294
Which bacteria allows for the engineering of transgenic plants
Agrobacterium tumefaciens
295
What process causes crown galls to form
The pTi plasmid contains T-DNA that is transferred into the plant cell through the action of the vir gene products
The DNA is inserted into the plant genome and expression leads to production of phytohormones and opines that result in plant cell proliferation
The bacteria then reside in the tumour and use the opines as nutrients
296
What triggers the sensor in the bacterial cell membrane to transcribe vir genes for the dna transfer
Phenolic compounds produces from wounded plants
297
How can plant genomes be modified using the Ti plasmid
Exchange genes in the Ti plasmid with transgene of interest
298
How does the glyphosate herbicide work
Inhibits EPSP synthase, which is important for amino acid synthesis
299
How is Bacillus thuringiensis used to engineer traits into plants
The bacteria produce Bt toxins that are harmful to insects from cry genes
Plants engineered to express Bt toxin to be resistant to insects
300
What is the refuge strategy used for resistance management of Bt crops
Resistant and vulnerable populations of insects will mate and produce offspring that are less resistant than if both parents were resistant
Grown non Bt crops next to Bt crops so there are populations of resistant and non resistant that can mate
301
Biofortification
Engineering increased nutrient levels in crop plants
| Ex. Golden rice
302
How is the synthetic Mycoplasma mycoides genome synthesized
Small 1kb fragments that overlap are synthesized and then assembled into larger and larger units to produce a synthetic genome
303
How is the synthetic M. mycoides genome characterized
Rare restriction enzyme cut sites are added to the genome, then electrophoresis is preformed with the synthetic and the original plasmid
304
Applications of yeast 1.0
Over express single genes
Complex gene modifications
a DNA assembly host
Capture of large DNA fragments
