Midterm 1 Flashcards
(177 cards)
1
Q
Main difference between bacteria and archea
A
Bacteria have peptidoglycan in cell wall
2
Q
Strain
A
Descendants of a single pure culture
3
Q
Species
A
Group of strains with similar traits
4
Q
What does a simple stain show
A
Size, shape, morphology
5
Q
Hyperthermophiles
A
High temperature, branched saturated membrane
6
Q
Psychrophiles
A
Low temperature, unsaturated membrane, fewer H bonds
7
Q
Acidophiles
A
Low pH, pump H+ out of cell
8
Q
Alkaliphiles
A
High pH, increase H+ in cell, produce acidic metabolites
9
Q
Comensals
A
One benefits, other is unharmed
10
Q
Differential media
A
Distinguish what bacteria possess certain traits by interaction with media
11
Q
MacConkey Agar selects for…
A
Gram Negative Cells
12
Q
MacConkey Agar differentiates….
A
Lac+ from Lac-
13
Q
Binary Fission
A
Primary reproduction of bacteria
2 daughter cells from mother
14
Q
Steps of binary fission
A
- DNA replication
- Elongation
- Septum forms via divisome
- Cells split
15
Q
4 growth phases of bacteria
A
- Lag
- Log
- Stationary
- Death
16
Q
Lag phase
A
Nutrients/DNA being replicated, cells not splitting yet
17
Q
Log phase
A
Cells rapidly split and number increases exponentially
18
Q
Stationary phase
A
Nutrients are low so growth slows
Cell density high
19
Q
Death phase
A
Cells degrade
Months to years
20
Q
Counting chamber
A
Manually counts cells/mL from a plate
Live and Dead cells
21
Q
Plate counting
A
Manually count colonies from a plate
CFU (collony forming unit)
Only shows viable cells
22
Q
Limitations to plate counting
A
Colonies can blend together
1 colony can come from multiple cells
One cell can only make one colony
23
Q
Serial dilutions
A
Make plate counting easier to count/more accurate
24
Q
Cell mass methods
A
- Dry weight
- Turbidity
25
Dry weight mass
Will include live and dead cells
26
Turbidity
Uses spectroscopy
Based on absorbance/scattered light
Includes dead cells
27
Hypertonic solution
Water leaves cell
28
Hypotonic solution
Water enters cell
29
Compatible solutes
For hypertonic solutions
- Prevents escape of water from cell
30
How does a cell react to a hypotonic solution
Mechanosensitive channels
1. Water enters cell
2. Cytoplasm stretches
3. Channels open
4. Solutes leave cell
Osmotic pressure relieved
31
Damage caused by pH changes
Cytoplasmic membrane, protein activity
32
How is cytoplasm pH maintained
Importing or exporting protons
33
What group exports protons
Acidophiles
Inside pH is too low (acidic)
Therefore, make more basic
34
What group imports protons
Alkalphiles
Inside pH too high (basic) therefore, make more acidic
35
What do hyperthermophiles have that others don’t
Most ether lipids
36
Levels of temperature bacterium
Psychrophiles
Psychrotrophs
Mesophiles
Thermophiles
Hyperthermophiles
37
What temperature does mesophiles like
Human body temperature
~37C
38
What are most psychrophiles responsible for
Refrigerated food spoilage
39
What are most mesophiles responsible for
Human pathogens
40
What role does oxygen have with bacteria
Essential for some, toxic to others
41
How does oxygen damage some bacteria
Forms Reactive Oxygen Species (ROS)
Oxidizes sensitive groups
42
Reactive Oxygen Species do what
React with proteins lipids, nucleic acid
43
Remembering why oxygen can be toxic
H2O vs H2O2
44
How do bacterial enzymes help protect against ROSs
Break down molecule/change it
2H2O2 -> 2H2O + O2
45
Obligate aerobes
Need oxygen
46
Obligate anaerobes
Grow without oxygen
47
What does oxygen kill
Obligate anaerobes
48
What does oxygen do to facultative anaerobes
Beneficial, not essential
49
What does oxygen do to aerotolerant anaerobes
No impact
50
What levels of oxygen do microaerophiles need
Low Oxygen
Can’t survive atmospheric levels
51
Testing Oxygen sensitivity
Top is oxic
Bottom is anoxic
Wherever cells end up in tube show ideal oxygen levels
52
Autoclaving
High pressure steam
Sterilizes
53
Pasturization
Kills pathogens with moderate heat
54
What does cold do to bacteria
slows metabolic activity
55
What effect do hypertonic conditions have on microbial growth
Dehydration slows microbial growth
56
What do extreme pH conditions do to microbial growth
Impacts protein function and slows growth
57
What products have general targets
Disinfectants and antisepctics
58
Disinfectant
Used for objects
59
Antiseptic
Used on live tissue
60
What have specific targets
Antibiotics
Targets are specific to bacteria
61
Oligotrophic environment
Low nutrients
Bacteria activate stringent response
62
Response to oligotrophic environment
Slowed metabolism, increased protein production to protect cell/dna
Persister cells and endospores can form
63
Persister cells
Growth arrested bacterial cells
Resistant to antibiotics
64
Endospores
Form inside a vegetative mother cell
Different structure, same genetics
Released via lysis
65
Resistance of endospores
Highly resistant to UV, heat, desiccation
Protected against chemicals, antibiotics, phage
66
Advantage of endospores resistance
Better survival in poor conditions
Can reform vegetative cells in proper conditions
67
What does the core of an endospores contain
Nucleotide
Ribosomes
Etc
68
What surrounds an endospore core
Cortex (peptidoglycan)
Coat (Protein)
Exosporium
Impermeable
69
Endospore formation
1. Cell division
2. Septum forms
3. Forespore develops
4. Forespore engulfed
5. Cortex forms
6. Coat forms
7. Lysis
70
Planktonic
Free floating (bacterium in lab)
71
Biofilm
Communities of bacterium forming a matrix (in nature)
72
Formation of biofilms
1. Quorum sensing
2. Autoinducer secreted (proportion relative to amount of cells)
3. High AI = pili made
4. Extra cellular polymeric substance (EPS) made
73
Planktonic to Biolfilm
1. Adhesion to surface -> sessile
2. Cell division
3. Cells stick and make EPs
74
Bacterial adhesion to host cells is
Specific via adhesions
75
Bacterial adhesion to abiotic surfaces is
Non-specific via bacterial components
76
What is the EPS
Slimy matrix, helps attach bacteria
Traps nutrients
Secreted or released via death
77
What kind of gradient formed by biolfilms
Oxygen gradient
78
Explain oxygen gradient of biolfilms
Surface = more oxygen = more nutrients = more metabolically active
79
Innate immune response
Nonspecific but fast
80
Adaptive immune response
Specific but slow
81
Chemical mediators
Promote inflammation, opsonization, make pores in cell wall
82
Opsonization
Help phagocytes recognize bacteria
83
Opsonization process
1. C3b binds surface
2. Receptors on phagocyte recognize c3b
3. Phagocytoses
84
Dendritic cells
Degrade antigens, activate T and B cells
85
Infection stages
1. Adhesion
2. Proliferation
3. Invasion
4. Tissue damage
86
Active penetration
Virulence factors
87
Passive penetration
Unrelated event (broken skin)
88
How do pathogens avoid detection
Intracellular pathogens
89
How do pathogens avoid recognition
Modify, decrease, hide antigens
90
Endotoxin
Lipopolysachharide (LPS)
Released if cell is listed
Can lead to sepsis
91
Exotoxins
Secreted
Ex. Neurotoxins
92
Quinolones/fluoroquinolones
Target topoisomerase of bacterium
93
narrow host range
Closely related species can replicate plasmid
94
Broad host range
Plasmid can be replicated in many species
95
How are plasmids classified
Accessory genes
96
Resistance plasmids
Protect bacteria against antibiotics
97
Virulence plasmids
Genes for virulence factors
98
99
Example of virulence plasmids
Enterotoxigenic E.Coli (ETEC)
100
What does ETEC plasmid encode for
Pili and toxins
101
Conjugation plasmids contain what
Sex pilis genes, MOB genes
102
What do MOB genes do
Encode proteins
Deliver plasmid into pilus
103
Mobilizable plasmids
MOB genes, no sex pilus genes, needs pilus from other cells
104
Transposable elements
Nucleic acid that can be transferred between DNA molecules (transposition)
Within chromosome
Chromosome to plasmid
105
Simple transposition uses what mechanisms
Cut and paste
106
replication transposition uses what mechanisms
Copy and paste
107
Transposable elements
Insertion sequence
Inverted repeat
108
Insertion sequence does what
Encodes transposase
Has inverted repeats on either end
109
What do inverted repeats do
Recognition sites for transposase
110
What does transposase do
Cuts DNA at IRs for transposition and inserts
111
What are direct repeats
Repaired dna flanking IRs after transposition
112
Unit transposons have what
IRS
Transposase gene
Resolvase gene (or others)
Accessory genes
113
Significance of transposons
Prevent inactivation of genes in new chromosome, transfer accessory genes
114
What do conjugation genomic islands encode
Excision, conjugation, integration
115
What do mobilizable genomic islands encode
Excision, integration
116
Pathogenicity islands do what
Carry virulence factors
Turn a safe cell into a pathogen
116
What must new DNA do to be retained
Integrate into genome
OR
Replicate apart from genome
117
Example of conjugation
F factor
118
Steps of Conjugation: F factor
1. Donor cell expresses sex pilus
2. Attaches sex pilus to recipient cell
3. Protein changes in pilus convert it to a type 4 secretion system (T4SS) - retracts
4. Relaxosome cuts at oriT site - replication
5. MOB genes encode coupling factor - pulls dna to T4SS
6. DNA enters recipient
7. Replication
119
What is transferred when making an Hfr cell
Bacterial chromosome and F factor
Recombines
120
What is transferred from an Hfr cell
Bacterial chromosome and F factor
Makes F’
121
Transformation requires what
COM proteins
122
what can trigger competence
Cell signalling
Nutritional stress
DNA damaging agents
123
Process of transformation
1. Secrete competence-stimulating peptide (CSP)
2. Threshold met = receptor activated
3. Com genes transcribed
124
Why is there a threshold for CSP
Makes sure there are other cells present for exchange
125
Com proteins
Transformation pilus
Membrane receptor
Nuclease
Transport Complex
126
Transformation pilus
Binds dsDNA
127
Membrane receptor
Binds dsDNA at other end and attaches it to cell surface
128
Nuclease
Cuts dsDNA to make ssDNA
129
Transport complex
Sends ssDNA into cytoplasm
130
What does RecA do - lac operon
Catalyzes recombination of ssDNA
131
Artificial competence
Lab induced competent bacteria
132
2 methods of artificial competence
1. Chemical (calcium chloride and heat shock)
2. Electroshock
133
What is the name of a phage that mediates transfer
Transducing particle
134
Lyric cycle - phage
1. Absorbtion
2. Injection
3. Degradation of host dna
4. Protein synthesis and packaging
5. Lysis
135
Generalized transduction
Randomly incorporating pieces of host dna into phage during lytic cycle instead of lytic dna
Forms transducing particle
136
What can a generalized transducing particle do
Inject dna, no lytic cycle
137
Lysogenic cycle - phage
1. Absorbtion
2. Injection
3. Integration
4. Replication of cells
5. Trigger causes lytic cycle to begin
138
Specialized transduction
Contains bacterial dna from beside excision site of phage dna
139
Lysogenic conversion
Conversion of Lysogenic phenotype via prophage
140
Prophage
phage dna
141
Extracellular vesicles
Contains cargo
Gram negatives
142
Steps of pathogensis
1. Sense host environment
2. Make needed proteins for attachment
3. Evaded immune system
4. Kill host cells
143
Sigma factors
Guide RNAP to promoter
144
Closed complex - transcription - occurs when
RNAP holoenzyme binds to promoter
145
Open complex - transcription - occurs when
RNAP unwinds DNA
146
2 types of terminators
Factor dependent (Rho)
Intrinsic (Hairpin)
147
Constitutive genes
Essential genes, always needed
148
Negative transcription control uses what
Repressors
149
Riboswitch - transcription
Leader region - 2 conformations
Allows or prevents transcription to continue
Requires metabolite or ligand
149
Process of a transcription riboswitch that is usually off
Metabolite forms anti terminator
Transcription continues
150
Process of a transcription riboswitch that is usually on
Metabolite forms anti-antiterminator
Termination stops
151
What is essential for bacterial replication
Ribosomes - translation
152
What do many antibiotics target
Ribosomes
153
Initiator tRNA
First tRNA needed
Charged with fMET in bacteria
Anticodon binds to start codon
154
What is responsible for charging tRNA correctly
Aminoacyl-tRNA synthetases
155
What bond binds amino acid with tRNA
Reactive ester bond
156
What binds are formed between aminos in tRNAs
Peptide bonds
157
Initiation of translation
1. 16s bind to RBS
2. Initiator binds to start codon in P site
3. Initiation factors help if needed
4. Forms 30s Complex
5. 50s joins 30 S
158
Elongation - translation
1. EF-Tu delivers tRNA to A site
2. Anticodon binds
3. Peptide bond formed (PTC)
4. Translocation (EF-G)
159
Termination - Translation
Stop codon - release factors
160
Tetracyclines
Bind to A site, block delivery
Bacteriostatic
161
Bacteriostatic
Inhibits growth, does not kill
162
Macrolides
Bind 50 S, block E site
163
Lincosamides
Binds 50S A site
Blocks peptide bond formation
164
2 conformations of riboswitch - translation
Sequester
Anti-sequester
165
Sequestor
Blocks RBS
166
Anti-sequestor
RBS available
167
Cis-encoded sRNA
Matches template strand
168
Trans-encoded sRNA
From other DNA
169
How does sRNA impact translation
Binding RBS: block initiation
Binding gene: block elongation
Binding Leader: prevent sequestor
Binding mRNA: degrade mRNA
170
RyhB sRNA
Fur: repressor
Fe2+: co-repressor
171
Limited Fe2+: what happens
RyhB binds mRNA of non essential proteins -> degradation -> more iron for needed protein
172
High Fe2+: what happens
Fe2+ binds to Fur, does not translate ryhB, no mRNA degraded
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174
Proteolysis
Enzyme, transcription/translational factors
Cleave one part of synthesis, limits production of protein
175
Multilevel regulation example
RpoE: sigma factor
Binds to RNAP
Controls damage repair genes
RseA: anti-sigma factor
Prevents RpoE from binding RNAP
Regulates when damage repair genes are coded
