MICR 221 > Midterm 1 > Flashcards

Midterm 1 Flashcards

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1
Q

Bacteria

A

Prokaryotes
DNA in cytoplasm
Lack membrane bound organelles
Single celled

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2
Q

Eukaryotes

A
  • DNA surrounded by nuclear membrane
  • Membrane bound organelles
  • Single or mulit-cell
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3
Q

Bacteria vs Archaea

A

Similar structure and metabolism
Major differences include:
- Cell wall components
- Peptidoglycan
- Transcriptional and translational components
- Types of lipids in membrane

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4
Q

Strain

A

descendants of a single pure microbial culture
- Have genetic differences

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5
Q

Species

A

group of strains with similar properties

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6
Q

Staining

A

Simple staining - shows size, shape and arrangement of cells
Differential staining - differentiate based on type of cell wall (gram staining), or other structures
- Gram pos retain violet because of thick peptidoglycan while gram neg retain counterstain

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7
Q

Bacterial Morphology

A

Cocci - spherical
- Diplococci
- Strephtococci (chains of spheres)
- Staphylococci (clumps of spheres
Bacilli - rods
Spirals

Shape can impact things like
- Motility
- Pathogenesis
- Ability to evade predators and immune system

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8
Q

Hyperthemophiles

A

Grow at very high temperatures
Membranes more viscous (less fluid), and contain saturated fatty acids (little double bonds)
Thermostable proteins
More intramolecular forces
Eg. taq polymerase

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9
Q

Psychrophiles

A

Grow at low temperatures
- Eg. brine veins in arctic ice
Make cryoprotectants, antifreeze proteins
- Prevents ice from forming in cytoplasm
Membranes have more unsaturated fatty acids (more double bonds)
- More fluid
Proteins more flexible
- Less intermolecular forces

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10
Q

Acidophiles

A

Grow at low pH
Keep cytoplasm neutral by h+ exclusion pump
Surface proteins acid stable

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11
Q

Alkaliphiles

A

Grow at high pH
Increase H+ uptake
Produce acid metabolites
Extracellular enzymes work at high pH

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12
Q

Commensals

A

one organism benefits whiles the other doesn’t but is not hardest

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13
Q

Defined Media

A

Synthetics - known composition of materials
Can be used to study nutritional needs

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14
Q

Complex Media

A

Contain partially hydrolyzed animal tissues, milk, yeast
Composition not fully defines
Very rich
Can support many species
Useful for unknown nutritional requirements

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15
Q

Differential Media

A

Distinguishes between different kinds of bacteria

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16
Q

Selective Media

A

Supports growth of certain species but inhibits growth of others

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17
Q

MacConkey agar

A

Selective for gram neg
- Bile salts
Differential
- Bacteria that ferment lactose
- pH indicator turns red

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18
Q

Binary Fission

A

Chromosome replicated
Cell elongates
Septum forms (cell well pinching inwards). Chromosomes partitioned
Daughter cells separate

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18
Q

Generation time

A

Doubling time
Time required to double population

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19
Q

Growth Phases

A

Lag Phase
- Acclimating to conditions
- Metabolically active
- Preparing for replication

Log Phase
- Cell replication
- Metabolically active

Stationary Phase
- Growth stops
- Waste accumulates
- Nutrients limited
- Balance between division and death

Death Phase
- Nutrients depleted
- Cell death

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20
Q

Direct Counting

A

Living and dead cells appear similar
Eg. Petroff Hausser

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21
Q

Plate Counting

A

Add sample to plate and count colonies that grow
Only viable cells counted/grow
Colony forming unit CFU
Once cell can make one colony, but multiple cells can make one colony
Smaller number than direct counts but only viable

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22
Q

Cell Mass Measurement

A

Number of genome copies
Metabolic activity
Cell mass
Dry Mass
Turbidity (liquid sample)

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23
Q

Spectrophotometer/Turdidimetry

A

Number of cells based on light absorbance
More viable cells mean more light absorbed
More light absorbed means higher OD (optical density

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24
Osmolarity
Isotonic - no net movement of water Hypertonic - loss of water - Plasmolysis - Combat by making compatible solutes to increase cytoplasmic osmolarity Hypotonic - gain of water - Osmotic lysis from swelling - Mechanosensitive channels to release solutes when cell swells
25
Temperature
Bacteria can’t control internal temperature Protect against environment based on membrane viscosity High temp saturated and more viscous Low temp less saturated and less viscous
26
Oxygen
Obligate aerobes Obligate anaerobes Facultative anaerobes - can survive with oxygen but not needed Aerotolerant anaerobes - oxygen does not impact them Microaerophiles - need low oxygen level. Can’t survive at atmospheric levels
27
Oligotrophic Environments
The normal environments for bacteria Low nutrient levels Lead to competition
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Starvation
Nutrient limitation activates stringent response Cell metabolism decreases Downregulated growth Upregulated stress response genes - ensure survival until nutrients are available Make proteins that protect DNA, cells walls and the cell. Protect against toxic chemicals and damage
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Persister Cells
Starvation can promote the formation of persister - Growth arrested - Identical to normal cells Formed under stress conditions Less susceptible to antibiotic - Antibiotics target growing cells - Can cause recurrent infections
30
Endospores
Formed from starvation Mostly gram pos cells Different structural composition - Same DNA Metabolically inactive - More resistance to antibiotics because not growing Endospore forms inside vegetative mother cells - Mother is growing - Endospore lysed out Highly resistant to heat and light Protected from chemical, antibiotics and phage - Impermeable membrane - Metabolically inactive Extreme measures needed to kill - Ex. autoclaving Regenerates vegetative cells under certain conditions
31
Endospore Structure
Core - Contains nucleoid, ribosome etc - Proteins protect DNA from heat, light and chemical damage Outer walls composed of cortex (peptidoglycan), coat (protein layers) exosporium. - Cortex and coats are impermeable
32
Endospore Formation
Septum formed and pinched off to form a forespore Phagocytosis of forespore Cortex formation (peptidoglycan) Coat formation Lysis of mother cell to release endospore
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Biofilms
Cells embedded in slimy matrix of extracellular polymeric substance - Made of glycoproteins, polysaccharides, DNA and other - Secreted by cells or released in death
34
Biofilm Formation
Quorum sensing to induced cooperative behaviour Cells secrete autoinducer Concentration related to number of cells Autoinducers are sensed by cells and control gene expression - Upregulated formation of extracellular polymeric substance production or genes involved in attachment (pili)
35
Growth in Biofilm
Matrix is highly nutriated and hydrated on outside Matrix traps nutrients Cells near surface can access more nutrients - More metabolically active Limited nutrients on inside of biofilm - Persister cell from starvation - Favour anaerobic cells Cells less accessible by predators and immune cells - Persister cells less susceptible to antibodies
36
Innate Immunity
Physical barriers - skin, mucous membrane Phagocytes - engulf and destroy bacterial cells Chemical Mediator - promote inflammation, form holes in cell walls, help phagocytes recognize bacteria with complement protein(Opsonization)
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Opsonization
- Complement protein C3b binds to surface of bacterium - Phagocytes have complement receptors - Leads to phagocytosis
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Adaptive Immunity
Dendritic cells degrade bacterial antigens DC activate T cells and B cells - B cells make antibodies that bind to antigen Antibodies help phagocytes recognized which cells to attack
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Virulence
Severity of disease caused by microbe Pathogen have virulence factors - features of pathogens that inc ability to damage tissue
40
Major Components of Infections
- Adhesion - Proliferation - Invasion - Tissue damage
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Invasion
Active Penetration - involves virulence factors - ex. enymes degrades ECM Passive Penetration - enters injury
42
Endotoxin
* Lipopolysaccharide (LPS) * Released if bacterium is lysed * Systemic effects (fever, shock, etc) * Activates severe response, may lead to septic shock
43
Exotoxin
- Secreted - Target host cell function - May be tissue specific
44
Immune Evasion
Avoid detection Avoid recognition - Decrease antigen production - Modify antigenic structure - Hide antigen
45
MRSA
Methicillin-resistan Staphyloccus aureus - Acquired mecA gene - Less suseptible to beta-lactams
46
Acquiring New DNA
- Adapt to selective pressures - Horizontal gene transfer - New DNA must integrate or replicate independently, or is lost
47
Recombination
Single or double crossover Homologous recombination - DNA with similar sequences Site-specific recombination - DNA without extensive homology
48
Chromosome Replication
Replisome starts at origin of replication - AT rich Chromosome is circular - Replication is bidirectional:two replication forks Produces catenated (circles linked) - topoisomerase form double stranded DNA breaks to separate rings
49
Quinolone and Fluoroquinolone Antibodies
Quinolone binds to the topoisomerase after is has made a double stranded DNA break, preventing it from repairing the break
49
Mobile Genetic Elements (MGEs)
Genetic material that can be transferred between cells - Plasmids - Transposable elements - Genomic island
50
Plasmid
Circular DNA Replicate independently from chromosome Multiple copies of same plasmid in the cell
51
Narrow Host Range
Plasmid can be replicated in closely related species - Plasmid carries fewer genes needed for replication
52
Broad Host Range
Plasmid replicated in many different species - Multiple origins of replication Plasmid encodes proteins needed for replication and transfer
53
Types of Plasmids
Resistance Plasmid - protect again antibiotics Virulence Plasmids - Carry genes for virulence factors
54
Types of Transposable Elements
Insertion sequence: - Only contain elements needed for transposition - transposase gen, inverted repeats, flanked by direct repeats Unit Transposons: - Transposase gene - Inverted repeated at both ends - May have accessor genes between IR. ex. antibiotic resistance
55
Simple Transposition
- Transposase produced - Transposase cuts DNA at inverted repeats - Cut transposable element enters new DNA
56
Genomic Island
Results from insertion of TEs, plasmids, other MGEs into the chromosome - Improve fitness - some encode virulence factors (pathogenicity island)
57
Conjugation
Direct transfer of DNA between bacterial cells via sex pilus -ex. F factor
58
F factor Mediated Conjugation
- Donor (F+) sex pilus attaches to recipient (F-) - Sex pilus retracts, pulling cells together - Pilus converts to type 4 secretion system - Relaxosome cut plasmid at oriT - Cust F factor relaxase into recipient making 2 F+
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HFr
F factor integrates into chromosome through recombination
60
F' Conjugation
F' is an F factor that has some chromosomal DNA when removed from Hfr - F- turns into F' through conjugation
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Transformation
Bacteria acquire DNA from environment - DNA will be integrated or degraded
62
Competence
State of being able to take up DNA Can be triggered by: - Cell - cell signalling - Nutritional stress - DNA damage
63
Competence Mechanism
Transformation requires competence proteins (Com proteins) - Transcribed when high conc of competence stimulating peptides are secrete - Transformation pilus releases
64
S. pneumoniae Competence
- Competence stimulating peptide secreted and competence proteins transcribed - Transformation pilus releases and binds to dsDNA - Membrane receptors bind dsDNA to cell surface - Nuclease cuts dsDNA into ssDNA - Transport complex transports ssDNA which is integrated or degraded
65
Artificial Competence
Treated with calcium chloride to mask DNA negative charge - Heat shocked to increase membrane permeability
66
Transduction
Transfer of DNA between bacteria by bacteriaphages (viruses)
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Bacteriophage Replication Cycles
Lytic cycle - Virus immediately replicates, lyses host cell Lysogenic Cycle - Viral DNA integrated into chromosome - Phage is dormant and not replicating - Forms prophage - Can reemerge under certain conditions
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Lytic Cycle
- Phage absorbs to cell and injects DNA - Degradation of host DNA and replication of phage DNA - Phage capsids produced - DNA packages into capsids and phage assembles - Phages lysed out
69
Generalized Transduction
- During the lytic cycle DNA is randomly packaged into capsids - Sometime host DNA is packages and horizontally transferred
70
Specialized Transduction
Errors can occur when prophage excise from host DNA, taking some DNA with them - prophage DNA and some chromosomal DNA packaged into transducing particles
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Lysogenic Conversion
- prophage modifies host cell to protect itself - removed receptors needed for phage infection - Become immune to similar phage - Prophage sometimes produce toxins and antibiotic resistance
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Transcription Intitation
Sigma factors proteins in RNA pol recognizes promoter (-35 - -10) and helps bind - RNA pol unwinds DNA forming open complex - sigma factor leaves
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Transcriptional Termination
Rho factor termination: Intrinsic Terminators: - inverted repeats followed by poly T tract
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Instrinsic Terminators
Inverted repeats of mRNA form hairpin structure after transcribed - loop causes RNA pol to stall and release at poly u track
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Regulation of lac Operon
- Allolactose is inducer molecule - Allolactose bind to lacI repressor, preventing it form binder to operator
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Regulation of trp Operon
tryptophan is co repressor - When tryptophan is high it binds to repressor, causing the repressor to bind and strop production of tyrptophan
77
Regulation of ara Operon
Arabinose is a co-activator that binds to araC dimer - when unbound araC bends DNA prevent transcription - arabinose prevent DNA bending
78
Riboswitch
mRNA leader region that can adopt two different conformations - terminator forms to stop transcription - anti-terminator formed to allow transcription. - ligand can induce formation of anti and anti-anti terminators
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Streptomycin
First antibiotic discovered - effective against gram negative - tuberculosis - aminoglycoside antibiotic targets ribosome
80
Aminoacyl-tRNA Synthetase
Charge tRNA with correct amino acid Anticodon binding domain: - recognizes tRNA anticodon Catalytic domain: - attaches amino acid to tRNA - required ATP
81
Transcriptional Elongation
EF-tu delivers tRNA to A site - energized with GTP Peptide bond formed in Peptidyl transferase center EF-G (GTP) push tRNA to P and E site
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Tetracycline Antibody
Binds to 30s subunit A site Basteriostatic - inhibits growth but doesn't kill
83
Lincosamides Antibody
Binds in A site of 50s subunit - disrupts peptidyl-transferase center
84
Macrolides Antibodies
Binds to 50s subunit exit tunnel - Prevent peptide from exiting ribosome, blocking sites
85
Antibiotic Resistance Mechanisms
By modifying ribosome: - erythromycin resistance methyltransferase By modifying antibiotic: - Acetyltranferase - Methyltranferase - Phosphotransferase
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Translational Riboswitch
Determines accessibility of ribosome binding site or Shine-Dalgarno sequence - Sequestor - Anti-sequestor - ribosome available
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sRNA
Small RNAs - non coding - bind to mRNA to make double stranded and disrupt function
MICR 221
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