Midterm 1 Flashcards
1
Q
Name the 5 microbial pathogens
A
Bacteria Viruses Fungi Protozoa Worms
2
Q
What is the definition of a bacterial pathogen?
A
A microorganism that causes pathology in a percentage of normal, non-immune hosts by manipulating cell biological processes and by avoiding or manipulating host innate immunity
3
Q
What is an opportunistic pathogen?
A
A microorganism that does not cause disease in a healthy host, but only in individuals whose normal defense mechanisms are compromised
4
Q
What is virulence?
A
A quantitative measure of pathogenesis
5
Q
LD50
A
(lethal dose 50), is the number of microorganisms (or amount of a toxin) required to kill 50% of the test animals.
6
Q
ID50
A
infectious dose 50, is the number of organisms (or amount of a toxin) required to produce an infection in 50% of the test animals.
7
Q
What are virulence factors and what are they defined by?
A
Components of the pathogen responsible for its ability to cause infection.
Defined by mutations in specific genes known as virulence genes
These result in lower virulence and therefore an increase in LD50
8
Q
What is an obligate pathogen? What is an obligate intracellular pathogen?
A
An obligate pathogen cannot (or has not) be found anywhere but in association with its host.
An obligate intracellular pathogen only grows inside host cells, and cannot be cultured extracellularly
9
Q
What is a facultative pathogen? What is a facultative intracellular pathogen?
A
A facultative pathogen can grow or survive in the environment as well as its host.
Facultative intracellular pathogens grow both inside and outside of cells and can be cultured on agar surfaces in the laboratory
10
Q
What are the 7 stages of pathogenesis?
A
(EECMIET) Encounter Entry Colonization (then signal transduction) Multiplication Invasion Evasion of host immunity Transmission
11
Q
Signal transduction of bacteria
A
Bacteria have sophisticated systems of signal transduction to detect and respond to changing environments; for example, oxidative/reductive stress, nutrient limitation, pH, presence/absence of glucose or amino acids
Two-component regulatory system of signal transduction
12
Q
Multiplication stage
A
The goal of every bacterium is to become bacteria & multiply
Compete with host for key nutrients and use those to grow
13
Q
What are lag, exponential and stationary phase?
A
Lag phase: adaptation into new media. No growth in cells
Exponential phase: abundance of nutrients and already adjusted to environment to grow exponentially
Stationary Phase: when bacteria stop growing because nutrients have been depleted
14
Q
Explain the evasion of host immunity stage of pathogenesis
A
Stealth strategy: Avoid being recognized (capsules)
Offensive strategies: Kill immune cells or interfere with cellular communication (toxins)
Infiltrate: Live inside immune cells: (intracellular pathogens)
15
Q
What are the three types of Horizontal Gene Transfer?
A
transformation, conjugation and transduction
16
Q
gram positive wall
A
Teichoic acids are sugar/amino acid polymers that give overall negative charge to the cell surface for nutrient uptake Thick PG layer, no outer membrane
Filled with teichoic and lipoteichoic acids
Cells lacking enzymes that make lipoteichoic acid have defects in shape and division.
17
Q
gram negative wall
A
PG is much thinner, OM is attached to PG via lipoproteins,
OM contains porins for permeability, outer leaflet has LPS
18
Q
What are the three features of LPS (lipopolysaccharide)
A
-Hydrophilic sugars protect the cell surface from bile salts, hydrophobic antibiotics, and complement activation
Hydrophilic sugars form a dense layer covering the cell
-Lipid A = fatty acids linked to glucosamine phosphate via ester amine bond aka endotoxin
-Core polysaccharide contains hexoses, heptoses and ketodeoxyoctonate (KDO)
-O-specific polysaccharide (O-antigen) is species- or strain-specific and is made of hexoses in branched units that repeat.
Involved in binding to plant/animal host tissues and evading the immune response.
19
Q
What are effector molecules of pathogenesis?
A
Proteins (often enzymes) that specifically interact with the host and secrete toxins
Effectors are secreted directly into cells by specialized secretion systems
They are the targets of vaccines
20
Q
What is the type 3 secretion system?
A
In Type III systems, virulence proteins are secreted directly from the bacterial cytoplasm into the cytoplasm of the host cell.
The needle structure punctures the host cell membrane to deliver secreted proteins that cause disease
21
Q
How do bacteria exploit host cell actin cytoskeleton?
A
They use it to mobilize around the cell
22
Q
How do bacteria grow extracellularly?
A
Polysaccharide capsule prevents phagocytosis by neutrophils allowing bacteria to grow extracellularly
An antibody breaks down the capsule to promote phagocytosis to destroy the bacteria (opsonization)
23
Q
How do bacteria grow intracellularly?
A
- Either promote their own uptake or exploit phagocytosis by macrophages (phagocytic cell)
- Once inside, they grow in either a modified vacuole or in the host cell cytosol
- Intracellular pathogens establish a unique replicative niche in which they replicate/live
- Immunity mediated by activated macrophages and cytotoxic T-cells
24
Q
What are three significances to the small size of bacteria?
A
- Faster diffusion rates and potentially faster growth rates
- High surface to volume ratio; no internal membranes; transcription and translation coupled
- Live as parasites of larger cells
25
What are some methods of classifying bacteria other than morphology?
- rRNA sequence are used in reconstructing phylogenies, due to the slow rates of evolution of this region of the gene (16S rRNA on 30S ribosomal subunit)
- Guanine and Cytosine (G+C) ratio: This serves to show that two organisms are not related.
- DNA homology: works for closely related species such as E. coli and Salmonella (about 50% DNA homology):
- Clinical differences: Yersinia. pestis and Y. pseudotuberculosis are 99% identical and are clearly the same species, but we still divide into two based on diseases.
- Gram stain (1884)
26
Gram stain
Gram - = pink/red
| Gram + = purple/blue
27
peptidoglycan
- Present in all bacteria with the exception of Mycoplasma (wall-less Gram-positive bacteria)
- Target of many antibiotics such as penicillin
- Allows bacteria to maintain high internal pressure without lysing
- The peptidoglycan layer in the bacterial cell wall is a crystal lattice structure formed from linear chains of two alternating amino sugars
- These are NAG and NAM (connected by glycan chains)
- Peptide attached to NAM contains both L- and D-amino acids
- Monomer of peptidoglycan = disaccharide pentapeptide
- DAP is unique to bacteria, and it helps to form peptide crosslinks in Gram-negative PG
- The glycan region is uniform and a site for lysosomal cleavage
28
autolysins
Enzymes, like lysozyme, that generate small breaks in PG during growth and synthesis. Bacteria have dozens of autolysins with different target sites
29
bacterial spores
Only found in two Gram-positive genera: Bacillus and Clostridium
-Spores are formed in response to nutrient deprivation
Spores help bacteria to survive by being resistant to extreme changes in the bacteria's habitat
30
Koch's Postulates
- The suspected pathogenic organism should be present in ALL cases of the disease and ABSENT from healthy animals -The suspected organism should be grown in pure culture
- Cells from a pure culture of the suspected organism should cause disease in a healthy animal
- The organism should be reisolated and shown to be the same as the origina
31
Prototroph
A bacterium that has no growth requirements other than the basic building blocks: C, N, P, S, K, Mg, Ca, Fe, and traces of Se, Mn, Co, Zn, and Cu
32
Auxotroph
A mutant that has a specific nutritional requirement for growth
33
Heterotrophs
like us; they require an organic C source (eg glucose)
34
Autotrophs
can get all of the C they need to build cell structures from CO2 in the air (CO2 fixation)
35
N fixation
- Animals, plants, and most microbes use NH4 + or NO3 – as their nitrogen source
- Only nitrogen-fixing bacteria can convert atmospheric N2 to NH4 + and assimilate it into cellular structures
- No pathogens can fix nitrogen
36
Turbidity
Cultures appear turbid/opaque because light passing through the sample is scattered by bacteria.
-optical density is proportional to cell number, but the exact relationship is different for each species due to cell size and shape.
-standard curve that relates OD to cell number counted by an independent method, such as a direct microscopic count.
Advantages: rapid, no sample destroyed
Disadvantages: does not distinguish between live and dead cells, or diff kinds cells
37
Exponential growth
```
N = N0 x 2^n
N0= initial cell #
n= # generations
Generation/doubling time g = t/n
-occurs when bacteria have enough of all required nutrients to duplicate their cellular structures and contents and divide (balanced growth)
```
38
Stationary phase
- Conditions in the batch culture or local environment change so that microbial growth is limited: cells run out of an essential nutrient cells and/or accumulate a toxic waste product
- No net increase or decrease in cell number (either not dividing, or divisions = deaths)
39
Lag phase
Occurs when a stationary-phase culture is diluted into fresh medium, Bacteria must sense new environment and synthesize many proteins needed for rapid growth, which were not produced during starvation
Occurs when cells are transferred from rich to minimal medium. Bacteria must sense new environment and synthesize specific proteins needed to produce the nutrients not already present in the culture medium
40
Psychrophile
grows around 4 degrees
41
Mesophile
grows at mod T, 20-45 degrees
42
Thermophile
grows around 60 degrees
43
Hyperthermophile
grows b/w 80-100 degrees
44
Halotolerant, Halophiles, Extreme halophiles
Ranging salty conditions
45
Obligate aerobes
must use O2 as terminal e- receptor
46
Obligate anaerobes
Must avoid O2
47
Facultative anaerobes
Can use O2 or not, but O2 is faster growth
48
Microaerophiles
O2 concentration must be low
49
Aerotolerant anaerobes
don't use O2 but are not harmed by it
50
Reactive Oxygen Species
ROS
When O2 is present, e-carrying molecules can donate e- to it (by accident) to create ROS
-can react with nucleic acids, proteins, and lipids to cause cell damage
Bacteria produce enzymes to detoxify reactive oxygen species (superoxide dismutase, Fe2+, Fenton rxn: catalase and peroxidase)
51
Iron-sulfer clusters
Upon oxygenation of earth, microbes were faced with two problems:
- iron availability as ferric iron is insoluble
- the oxidative stress caused by the Fenton reaction:
52
Bacterial biofilms
a group of bacteria enclosed in an adhesive, self-produced matrix composed of exopolysaccharides (EPS), proteins, and nucleic acids
- adhere to abiotic or living surfaces, or they may exist as free-floating communities (flocs) in aquatic environments
- have different growth rates, different transcriptional profiles, enhanced tolerance toward antibiotics, and enhanced interactions with other microbes
53
Average prot and gene
Prot: 33,000 da (33-kDa), 300 a.a.
Aa: 100 da
Gene: 1-kB, 3000 genes in genome
54
What are the 4 factors that influence gene expression and protein synthesis
- Transcription: Promoter strength
- mRNA half-life
- Strength of ribosome binding site
- Protein half-life
55
Operon
- Basic unit of transcription in bacteria with an average of 3 genes/operon
- Consists of a single promoter, one or more open reading frame(s), and transcriptional terminator
- Each gene has it’s own ribosome binding site (rbs)
56
Sigma subunit
σ subunit or σ factor attaches to the core enzyme and helps RNA Polymerase recognize and bind to the promoter region of a gene
57
What makes a strong promoter?
- Better match of promoter sequence with the consensus sequence for a sigma factor makes a strong promoter, which yields more binding by the σ factor and more tx of gene
- Worse match with consensus makes a weak promoter. Extra proteins (transcriptional activators) are often needed to turn on tx at weak promoters.
58
What do accessory transcription factors do?
- Accessory transcription factors (aside from RNAP and σ) promote or repress transcription of specific genes
- contain a DNA-binding domain and regulatory domain(s) that determine when the protein is active
- Often act as dimers and bind to direct or inverted repeats on DNA
- activator turns on tx of a gene, while a repressor blocks tx
59
What do modified nucleotides act as and what are they?
- When glucose is limiting, ATP is converted to cyclic- AMP (cAMP) by adenylate cyclase -When amino acids are limiting, bacteria synthesize (p)ppGpp from ATP and GTP/GDP by an enzyme called RelA
- Bacterial motility and biofilm formation are regulated by cyclic-di-GMP (c-di-GMP)
- Bacterial osmoregulation is controlled by c-di-AMP
60
Catabolite repression
allows the bacterium to use the most efficient carbon source first (often the one most easily fed into the glycolytic pathway-glucose)
61
Diauxic growth curve
- curve of cells grown on a mixture of glucose and lactose
| - Lag in growth occurs when glucose is gone, and cells must make new enzymes to use lactose
62
How does CAP/cAMP activation/co-activation work?
- In the absence of glucose, transcription of genes for alternative sugar utilization is activated by the catabolite activator protein CAP; Also called CRP (cAMP receptor protein)
- CAP is an activator, and cAMP is its co-activator
- Lactose is an inducer for the LacI repressor
63
What is the stringent response system and how does it work?
-During amino acid starvation, uncharged tRNAs accumulate in the cell.
-When an uncharged tRNA enters the A site of a translating ribosome, it is sensed by the ribosome-associated protein RelA.
In response, RelA synthesizes pppGpp from GTP and ATP or ppGpp from GDP and ATP
64
What does ppGpp do?
- Higher (p)pGpp induces a slow-growing state that helps the cell to survive amino acid starvation -Ie. reduce their growth rate and synthesis of macromolecules (DNA, RNA, protein), increase their synthesis and recycling of amino acids
- (p)ppGpp affects transcription, translation, replication, protein degradation, and other processes that are coordinated to respond to starvation
- inhibits chromosome replication
- (p)ppGpp binds to the active site of DnaG, the primase enzyme necessary for both the initiation and elongation phases of DNA replication.
- slows chromosome replication that has already started and prevents new rounds from starting (slows everything down to make more amino acids)
65
What is oxidative stress and how does it work?
- imbalance between the production of free radicals and the ability of the body to counteract or detoxify their harmful effects through neutralization by antioxidants
- OxyR is a hydrogen peroxide sensor
- sense oxidative species inside the cell and to trigger the cell's response, activating the transcription of genes involved in scavenging oxidative species
- Hydrogen peroxide causes oxidative stress
66
How does heat shock response work?
-RpoH is a transcription factor for heat shock genes
-RpoH gene: an mRNA, protein unfolding allows the transcription of DnaK chaperones
-DnaK: will promote the refolding or degradation of proteins
Steps to heat shock response: Heat Shock occurs→ melts stem loop on mRNA→ RpoH gene is translated→ RpoH binds to RNAP to promote tx of Heat Shock genes (ex: chaperones (DnaK)) → DnaK helps refold denatured proteins → When it’s done, DnaK binds to RpoH→ RpoH is degraded by a protease
67
What is the Sec pathway (general secretory pathway)
- Proteins destined for secretion have an N-terminal “signal sequence”
- SecA is the signature gene, although other Sec proteins required
- In Gram-negatives, proteins are secreted into the periplasm from cytoplasm
- SecY, SecE, and SecG form a protein-translocating channel in the membrane
- SecB chaperone binds the signal sequence of a fully synthesized protein and keeps it in an unfolded state for export powered by the SecA ATPase
- Used for OM proteins, lipoproteins, periplasmic proteins
68
Quorum sensing
- the ability of bacteria to communicate and coordinate behavior via signaling molecules.
- Autoinducers--the signaling molecules produced and used for quorum sensing.
- Gram negative: Acyl Homoserine lactones
- Gram positive: peptides
69
Minimal inhibitory concentration
lowest concentration of drug that inhibits bac growth so no turbidity
70
Minimal bactericidal concentration
lowest concentration that kills bac
71
Three main antibiotic targets
Cell wall syn
Prot syn
Nucleic acid biosyn
72
Beta-lactam antibiotics
- Bacteriocidal; only kill growing bacteria
- Act by binding to enzymes involved in peptidoglycan biosynthesis (penicillin binding proteins). This blocks transpeptidation and promotes activity of autolysins and lysis
- mimic the d-ala-d-ala
- Penicillin is the best example as it creates an intermediate that imitates the D-ala-D-ala residue of PG synthesis to block the transpeptidation stage
73
Penicillin selection of serine auxotroph
- Grow cells in minimal medium supplemented with 19 amino acids (but not serine),
- all cells, both wt and other auxotrophs, will grow except serine auxotrophs
- When cells are happily in exponential growth, throw in penicillin (or other cell wall antibiotic) --> wall damage in all growing cells, but not in serine auxotrophs.
74
Aminoglycosides
- protein synthesis inhibitors that target the 30S ribosomal subunit, resulting in misreading of mRNA
- Do not penetrate mammalian cell membranes
- Bacteriocidal: bacteria killed but not lysed
- Ex. streptomycin and gentamycin.
- Tetracycline: Targets 30S ribosome, bacteriostatic
- Chloramphenicol; Targets 50S ribosome, bacteriostatic
75
Nucleic acid inhibitor of DNA syn
- quinolones like naladixic acid are cidal and bind to DNA gyrase
- Single amino acid mutation in DNA gyrase leads to resistance.
- DNA gyrase uncoils DNA before it is transcribed
76
Nucleic acid inhibitor of RNA syn
- rifampin binds to beta subunit of RNA polymerase and is static
- Single amino acid mutations in RNA polymerase leads to resistance
77
B-lactams
Penicillin and ampicillin
| -blocks transpeptidation and promotes activity of autolysins and lysis
78
Nucleic acid inhibitors
Rifampin
| Naladixic acid
79
Prot syn inhibitors
- Aminoglycosides: streptomycin and gentamicin
- Chloramphenicol
- Tetracycline
80
Vertical gene transfer
when an organism receives genetic material from its ancestor, e.g. its parent or a species from which it evolved
81
Horizontal gene transfer
an organism incorporates genetic material from another organism without being the offspring of that organism
-Bacteria evolve mostly by acquisition of genes acquired by HGT
82
Describe the mechanisms of DNA acquisition? (HGT)
- Conjugation - requires a transfer mechanism and contact between donor and recipient cells
- Mediated by Transfer (Tra) proteins which encode, among other proteins, a pilus
- F-pilus is a complex retractable organelle that mediates bacterium-bacterium interaction.
- Regulated process b/c pili often act as phage receptors.
- Transformation - requires an ability (machinery) by the recipient to take up linear DNA from the environment.
- Ex: inserting plasmid into DNA
- Unnatural transformation of plasmid DNA: calcium and cold-shock induced.
- electroporation: Method for introduction of plasmid DNA into many different bacterial species simply by inducing holes in the cell membrane via electronic pulses.
- Transduction - requires bacteriophages that can transfer (transduce) DNA between donor and recipient cells.
83
How does Natural Transformation occur?
- Rec-dependent recombination: General or homologous recombination results from the genetic exchange between homologous DNA from two different sources. RecA is an enzyme necessary for this process.
- ~Competent~ recipient will take up foreign DNA. Then, it will incorporate the homologous portions of foreign DNA into its own through recombination mediated by the RecA enzyme.
- Small fragments are incorporated (about 15-kB);
- Requires a high degree of DNA homology)
84
Plasmids
a genetic structure in a cell that can replicate independently of the chromosomes, typically a small circular DNA strand in the cytoplasm of a bacterium
- Replication
- Transfer: Transfer (Tra) or mobilization (Mob)
- Size (from 2-kb to many hundreds of kb)
- Copy number: Number of plasmid copies in a cell
- Stable inheritance
85
Cloning vectors
- Antibiotic resistance genes derived from large plasmids encoding antibiotic resistance
- Replication functions from small, high copy plasmids (minus mobilization)
86
Shuttle plasmids
often have origin of replication (ori) that permits replication in E. coli and a second ori for replication in a second host species
Often incorporate Transfer (Tra) functions from wide host range plasmids, thereby allowing you to transfer by conjugation
87
Transposons
- jumping genes important for the evolution of multiple antibiotic resistance
- Transposition is Rec-independent
- transpose (hop) at a frequency of 10-3- 10-7 encode transposase
- Minimal target sequence specificity, bordering on random
- Like plasmids, often confer selective advantage
- Regulated: Controlled by transposase and its repressor.
- Generate polar mutations due to presence of transcriptional terminators
- Polar = downstream genes or operons
- Transposon insertion can create a stop codon where it did not previously exist. This will prevent transcription of downstream genes.
88
Transposon mutagenesis
- generate random (or semi-random) insertion mutations
- tag mutated gene allowing isolation and characterization of that gene and surrounding gene (Transposon goes in and messes up a gene. Then you want to find the messed up gene. If you know the sequence of the transposon, you can find the messed up gene and clone it.)
- If your transposon confers drug resistance, put it in a gene. Then expose that gene to the drug. Whatever doesn’t die took up the transposon and can be cloned.
- Low reversion frequency to wild-type phenotype
- generate polar mutations
89
Transposon library
- a collection of bacteria that contains multiple individuals each with a single transposon insertion.
- Screening a transposon library for mutants: replica plating
90
Lytic bacteriophages
Virus particle attaches to diff prot on CM --> Injection of viral DNA --> syn of nucleic acid and prot --> assembly and packaging --> make lysozyme and release
Takes 90 min, 1 goes in 200 come out
91
Lysogenic bacteriophages
- Viral dna is integrated into host dna = prophage
- Can lay dormant and replicate w host dna or thru induction become lytic
- Common in wild
- Adds virulence to bac --> clinically relevent
92
Phage conversion
phage incorporates virulence factor into host DNA making the bacteria a highly virulent pathogen
93
Phage transduction
- used as a method for strain construction and mapping
| - When a phage contains the host DNA and injects it into another bacteria where it recombines with the new host’s DNA
94
Pangenome concept
- Core genome (housekeeping)
- Chromosome (plasmids)
- Ribo, cell envelope, key metabolic pathways, DNA repli, nucleotide turnover
- flexible gene pool
- Genomic islands/islets, phages, plasmids, integrons, transposons
- Pathogenicity, Antibiotic resistance, secretion, symbiosis, degradation, 2dary metabolism, restriction/modification, transposases/Integrases
95
Pathogenicity island (PAI or Pis)
- a distinct class of genomic islands acquired by microorganisms through horizontal gene transfer.
- incorporated in the genome of pathogenic organisms, but are usually absent from those nonpathogenic organisms of the same or closely related species
- Often have different G+C content than chromosomal DNA
- Inserted into tRNA, or duplicated genes
- Associated with mobile DNA elements
96
Reporter
used in biological systems to quantitate gene or protein expression
-usually an enzyme that has properties making it easy to measure
Ex. lacZ encoding beta-galactosidase; phoA encoding alkaline phosphatase; GFP (green fluorescent protein)
97
What are the mechanisms of antibiotic resistance?
1. Endogenous resistance (Outer Membrane)
2. Multidrug transport
3. Spontaneous resistance
4. Inactivating enzymes
5. Target alteration.
98
Multi-drug resistance transporters
- Membrane proteins that actively transport a wide variety of structurally unrelated compounds.
- Found in all bacterial species.
- Play a role in active efflux of antibiotics and other toxic compounds.
99
Antibiotic resistance acquired by genetic change
- clinically relevant form of antibiotic resistance.
- Plasmids and transposons may encode one or more different antibiotic resistances
- thus selection for one antibiotic can lead to resistance to other antibiotics
100
Inactivation of antibiotics
-Beta-lactamase cleaves the β-lactam ring to render the antibiotic irreversibly inactive.
101
Explain how the targets of antibiotics can be altered to encode resistance
- Erythromycin resistance is mediated by methylation of an adenine on the 23S rRNA.
- Vancomycin resistance is mediated by changing the terminal D-ala-D-ala to D-ala-Dlactate or D-ala-D-serine
102
Persisters
In the presence of antibiotics, a small percentage of bacteria survive, but are not genetically resistant.
103
Transcriptional fusions
rely on the promoter of a target gene, but contain their own ribosome binding site and start codon.
Lac-fusions express betagalactosidase under the transcriptional control of another gene.
A fusion can be both transcriptional and translational
104
Translational fusions
in-frame fusions between two proteins, so that the promoter, ribosome binding site, start codon, and some or all of the coding sequence are fused in-frame with another protein.
A fusion can be both transcriptional and translational
105
Forward genetics
In bacteria, construct a transposon library
- Select for mutants affecting phenotype
- Identify site of insertion
106
Reverse genetics
- Start with genomic sequence
- Identify gene(s) based on homology that you hypothesize has important phenotype
- Introduce mutation: insertion, deletion, point mutation
107
TLR3
-Double stranded RNA (dsRNA)
-TLR3 forms a homodimer (two TLR3 molecules come together to bind ligand)
dsRNA binds inbetween the dimer
108
TLR5
homodimer recognizes bacterial flagellin
109
TLR4
homodimer recognizes LPS
110
TLR1 and TLR2
heterodimer of TLR1 and TLR2 binds bacterial lipoproteins
111
MyD88/Trif
Second messenger
| Phosphorylated by TIR domain of TLR
112
Innate Immune sensors
- Cytosolic nucleic acid sensors
- Nods (Detect peptidoglycan)
- Inflammasomes
113
NF-kB
Activated by NOD1/2, TNF alpha
| -cell death via apoptosis
114
RIG-I
- detects viral RNA with a 5’triphosphate
- most self RNA has a 7-methyl-guanosine cap, which does not bind RIG-I
- RIG-I signals by binding to a protein called MAVS --> Type 1 Interferons
115
cGAS
DNA sensor for viral infect
- (cyclic-GMP-AMP synthase) -binds dsDNA
- cGAS is an enzyme. When it binds dsDNA it is activated to produce a second messenger (cyclic-GMP-AMP) that binds to a protein called STING --> Type 1 Interferon
116
NOD1/2
cytosolic innate immune sensor proteins that detect fragments of peptidoglycan
When activated, NOD1 and NOD2 turn on NF-kB
117
NAIP5/NLRC4
- inflammasome which detects the cytosolic presence of specific bacterial proteins
- binds flagellin and forms a large complex called an “inflammasome” with caspase-1
118
C3a
C3a and C5a are complement proteins that attract phagocytes)
119
C3b
Opsonization
complement protein binds to bacterial surface and promotes phagocytosis of bacteria by complement receptors on phagocytes)
AKA complement binds bacteria, phagocyte finds complement→ phagocytosis of bacteria
120
C5a
C3a and C5a are complement proteins that attract phagocytes)
121
IL-1
pro-IL-1 cleaved by caspase-1
- Gasdermin D forms pores in CM to allow release of IL-1
- causes recruitment of Neutrophils
- fever
122
IL-8
actually chemokine
| attracts neutrophils
123
IL-10
-reduces inflammation
124
IL-12
Causes T cells and NK cells to make IFN gamma
125
TNF
activates NF-kB --> cell death
126
CDR
complementarity determining regions (highly variable loops that recognize antigen)
- light and heavy chains each have 3
- CDR1/2 in V gene segment
- CDR3 in V(D)J junction --> hypervariable bc joining not precise
127
VDJ
- The genes encoding TCRα and TCRβ undergo V(D)J recombination to produce a vast repertoire of diverse TCRs
- creates Ab diversity
- 5x10^13 total Ab diversity
- enzyme called the RAG recombinase, that cuts and joins DNA responsible
128
RAG
A special enzyme called RAG recombinase, that cuts and joins DNA, is required to carry out the process of V(D)J recombination
129
SCID
Mice or humans with a defective RAG recombinase fail to make B or T cells and have SCID (severe combined immunodeficiency)
130
caspase-1
protease
- cleaves pro-IL- 1 into its active and secreted form
- cleaves a protein called Gasdermin D -->forms pores in the plasma membrane that allow release of cleaved IL-1.
131
Gasdermin
Gasdermin pores also cause cells to die by “Pyroptosis
132
Complement
- Opsonization (C3b complement protein binds to bacterial surface and promotes phagocytosis of bacteria by complement receptors on phagocytes)
- AKA complement binds bacteria, phagocyte finds complement→ phagocytosis of bacteria
- Chemoattraction (C3a and C5a are complement proteins that attract phagocytes)
- Direct lysis of bacteria (the complement membrane attack complex (MAC) forms pores in bacteria, thereby killing them)
133
How do antibodies protect against infection?
1. Neutralization (inhibition or inactivation of the pathogen or its toxins)
2. Opsonization (promotion of phagocytosis)
3. Complement activation
134
Somatic hypermutation
- occurs especially upon the secondary or tertiary exposure to the same pathogen, and allows the generation of very high affinity antibodies (this process is called affinity maturation)
- To create more diversity after the process of V(D)J recombination is complete, B cells randomly mutate their heavy and light chain genes
135
Postulates of Clonal Selection hypothesis
- each lymphocyte bears a single type of receptor with a unique specificity
- Interaction b/w a foreign molec and a lymphocyte receptor capable of binding that molec with high affinity leads to lymphocyte activation
- The differentiated effector cells derived from an activated lymphocyte will bear receptors of identical specificity to those of the parental cell from which that lymphocyte was derived
- Lymphocytes bearing receptors specific for ubiquitous self molec are deleted at an early stage in lymphoid cell development and are therefore absent from the repertoire of mature lymphocytes
136
germinal centers
Special cellular structures in lymph nodes where somatic hypermutation and intense evolutionary competition occur
137
CD40
on B cells. Engages with CD40L on T cells and this along with cytokines from T cell activate B cell
138
Linked recognition
- how B and T cells recognize different parts of the same pathogen
- critical to allow for antibody responses to polysaccharide (non-protein) antigens
