Final Exam Flashcards
Cell wall synthesis inhibitors
Glycopeptides/lipopeptides- includes
vancomycin, daptomycin and teichoplanin
b-lactam antibiotics-
The four main
types are penicillins, cephalosporins,
carbapenams, and monobactams.
can function as a
barrier to certain antibiotics.
outer membrane
Porins-
proteins in the OM of Gram-
negatives that allow diffusion of nutrients
and other molecules.
how does outer membrane become antibiotic resistant?
mutations in porin genes limit permeability of small molecules like antibiotics
can function as a barrier (relatively rarely) to antibiotics
cytoplasmic membrane
_______ are composed of
membrane proteins that use energy to
pump small molecules out of the
bacterial cytoplasm.
efflux pumps
Two types of efflux pumps:
antiporters and
ABC transporters.
What 3 general ways can bacteria be resistant to antibiotics?
- limiting the antibiotic’s access
- enzymatic inactivation of the antibiotic
- modification or protection of the antibiotic target
enyzmes that cleave the
b-lactam ring of b-lactam antibiotics
b-lactamases
chloramphenicol acetyltransferases will add _____ to chloramphenicol, preventing it from ______
acetyl groups
binding to the 23s rRNA in the 50s subunit
examples of enzymatic inactivation of antibiotics are B-lacamases, _________ and ________
Aminoglycoside-modifying enzymes, Chloramphenicol and streptogramin
acetyltransferases
modification of b-lactams target occurs by-
alteration of the transpeptidase or
one of the other penicillin-
binding proteins (PBPs) in the cell.
what gene in Staph aureus encodes a modified PBP2?
mecA
Resistance to glycopeptide
antibiotics involves alteration of-
the peptide portion of peptidoglycan.
Bacteria resistant to glycopeptide antibiotics can have 3 enzymes that work together to confer resistance. name them and tell how they cause resistance:
VanH catalyzes conversion of pyruvate to D-lactate
VanA or B leads to formation of D-Ala-D-lactate instead of D-Ala-D-Ala (vancomycin’s target)
VanX cleaves any D-Ala-D-Ala that might have formed
Resistance to tetracycline involves-
“ribosome protection” or alteration
of the ribosome
Resistance to macrolides,
streptogramins, and lincosamides involves-
RNA methylases add a methyl group(s)
to 23S rRNA (part of 50S subunit)
Resistance to quinolones, rifampin, and streptomycin (an aminoglycoside) involves-
alterations (through mutation) of the
particular target of the antibiotic
Resistance to trimethoprim and
sulfonamide involves-
alterations (through mutation) of the enzymes in the tetrahydrofolate biosynthesis pathway.
resistance genes are regulated by: (3)
repression, translational attenuation, activation
name the way in which each gene is regulated: tetB- erm- blaZ- ampC- vanH/A/X-
- repression
- translational attenuation
- repression
- activation
- activation
what does each of these genes encode: tetB- erm- blaZ- ampC- vanH/A/X-
- TetB efflux pump
- RNA methylase
- b-lactamase
- b-lactamase
- vancomycin resistance
the 3 general mechanisms for horizontal gene transfer:
transformation, transduction, conjugation
what region of the F plasmid encodes conjugation proteins?
tra region
what is the origin of transfer in the F plasmid?
oriT
name the 5 general characteristics of plasmids:
Extrachromosomal Replicate autonomously Most are circular Often contain resistance genes May be self-transmissible or mobilizable
the plasmid R100 transfers via conjugation among which species?
Escherichia, Klebsiella, Proteus, Salmonella, and Shigella species
the resistance plasmid R100 confers resistance to what?
mercury, sulfonamide, streptomycin, chloramphenicol, tetracycline
what two ways does multi-drug resistance arise in bacteria?
1) A single mechanism that confers
resistance to multiple antibiotics
(e.g., multi-drug efflux pump).
2) Acquisition of a plasmid or other
conjugative genetic element that
contains multiple resistance genes.
How does a plasmid acquire multiple
resistance genes?
transposons or integrons
transposons-
segments of
moveable DNA that can insert into a
chromosome or plasmid independent
of homologous recombination.
integrons-
typically transposons
but they also contain an integrase
gene and an attachment (att) site.
integrons can supply resistance genes with ____ and ____
a promoter and integrase gene
Conjugative transposon-
second type
of conjugative genetic element .
Generally have a broader host range
than most plasmids.
if an antibiotic is improperly prescribed, it can select for resistance in _______. when properly prescribed but improperly used, it can select for resistance in _______
- normal flora
- the pathogen population
Tn5 and Tn3 are both
transposons
Point mutations, gene deletions,
or duplications, and chromosomal
rearrangements (all slow processes) occur at frequencies ranging from:
10^-6 to 10^-9 per nucleotide per generation in bacteria
what are 3 ways pathogen evolution occurs (mechanisms of genetic change and diversification):
- random genetic mutation
- phase variation
- Antigenic variation
how would phase variation benefit bacterial evolution?
On-off control of some bacterial genes, such as those encoding surface proteins, that allow response to rapidly varying environmental conditions.
what kind of phase variation occurs in Salmonella species?
flagellin protein
what alternative types of flagellin protein can salmonella use?
H1 or H2
- Frequency of salmonella flagellar phase variation is ~
10-4 per cell per generation.
Which gene, upon inversion, can activate or inactivate H1 flagellin/H2 flagellin
Hin invertase
in one orientation, a promoter is available to transcribe ____ and ______, but if Hin invertase flips the Hin gene, the promoter is flipped to the other side and ________ are no longer transcribed, allowing _____ to freely be transcribed
- H2 flagellin and H1 flagellin repressor
- H2 flagellin and H1 flagellin repressor
- H1 flagellin
Phase variation inn Bordetella pertussis involves what two proteins?
BvgS and BvgA
The BvgS and BvgA proteins compose a:
two-component signal transduction system that controls expression of a number of virulence genes
Phase variation in pertussis is mediated by:
a reversible mutation in the bvgS gene.
the reversible mutation that causes phase variation in pertussis is:
The result of this mutation is:
- addition or deletion of a GC base pair in a sequence region containing a string of 6 GC base pairs.
- a switch between BvgS+ and BvgS-
adding a GC pair to the bvgS gene switches it from ____ to ____. Removing that GC pair then switches it back.
BvgS+ to BvgS-
Phase variation in Neisseria species involves ____ proteins
Opa
Opa proteins are located in ________ in N. meningitidis and N. gonorrhoeae. They mediate _______________.
- the outer membrane
- adherence and invasion during infection
Each Neisseria species has multiple opa genes, any of which may be ____________
on or off at different stages during infection
opa genes contain _________ that cause_____________
- 5’ tandem repeats of (CTCTT)n
- high frequency slipped strand misrepair and thus frameshifts in the gene
Some bacteria have mechanisms that allow alternative forms of genes to be expressed in what is known as:
These variable forms of a gene are achieved through:
- antigenic variation
- gene shuffling
Gene shuffling mechanisms that allow alternative forms of some genes, such as those encoding surface proteins, to be expressed
antigenic variation
The result of antigenic variation is that:
a range of antigenically distinct forms of a protein can be produced, which helps the bacterium avoid the host immune system.
T4SS are divided into what 3 functional groups?
conjugative, DNA uptake/release (transformation), and effector translocation
What can Conjugative T4SS deliver between bacteria?
plasmids or transposons
What can Effector translocation T4SS systems deliver into eukaryotic cells?
DNA or protein
The Agrobacterium tumefaciens type 4 secretion system
Purpose:
Protein composition:
- delivers oncogenic DNA along with several effector proteins into plant cells.
- VirB1-VirB11 and VirD4
The Agrobacterium tumefaciens type 4 secretion system Energetic components-
Purpose-
- VirB4, VirB11 and VirD4
- are all ATPases.
The Agrobacterium tumefaciens type 4 secretion system Channel (core complex) components-
Purpose-
- VirB6- VirB10
- they form the channel through the bacterial cell envelope
The Agrobacterium tumefaciens type 4 secretion system Pilus-associated components-
VirB2 and possibly VirB3 and VirB5
The Agrobacterium tumefaciens type 4 secretion system transglycosylase is:
What does it do?
- VirB1
- localized hydrolysis of the peptidoglycan at the site of assembly of the type 4 secretion apparatus.
The Agrobacterium tumefaciens type 4 secretion system substrates:
T-DNA complex and effector proteins
The Agrobacterium tumefaciens type 4 secretion system T-DNA complex consists of:
single stranded T-DNA with VirD2 protein covalently attached at 5’ end
Where does the Agrobacterium tumefaciens type 4 secretion system T-DNA come from?
What genes does it contain?
- It comes from the T region of the Ti plasmid
- It contains an auxin production, cytokinin production, and opine synthesis gene
The Agrobacterium tumefaciens type 4 secretion system:
Which genes on the T-DNA are oncogenic?
auxin and cytokinin production
The Agrobacterium tumefaciens type 4 secretion system:
Besides the T-DNA genes, what genes exist on the Ti (Octopyne type) plasmid?
conjugative transfer, Opine catabolism, origin of replication, and virulence region
The Agrobacterium tumefaciens type 4 secretion system effector proteins are:
VirE2, VirE3, VirF, and VirD5
The Agrobacterium tumefaciens type 4 secretion system:
What effector protein binds to T-DNA?
When does it do this?
Why does it do this?
- VirE2
- upon secretion into the plant cell
- to protect the DNA from nucleases
The Agrobacterium tumefaciens type 4 secretion system:
Which two effector proteins have NLS?
VirD2 and VirE2
Disinfectants-
chemicals (generally)applied to
inanimate objects and surfaces.
Antiseptics-
chemicals applied topically to
living tissue or skin.
Antibiotics-
generally derived from microbial
sources and are administered either outside or inside the body.
Bactericidal-
term used to describe anti-microbials that kill bacteria.
Bacteriostatic-
term used to describe anti-microbials that stop or slow the growth of
bacteria.
The efficacy of an antimicrobial compound (whether it is cidal, static, or ineffective) depends on:
the properties of the target bacteria
What test is used to determine antibiotic sensitivity to an antibiotic?
Disc diffusion assay
The lowest concentration of antibiotic that will
prevent growth of the target bacterium.
Minimum inhibitory concentration (MIC)
b-lactams act as ___________ by binding irreversibly to _________ (one of several penicillin-binding proteins).
- suicide substrates
- transpeptidase
Random Cell wall synthesis inhibitors that aren’t beta lactams or glycopeptides:
fosfomycin, bacitracin, tunicamycin
Aminoglycosides-
What do they inhibit?
- includes kanamycin and
gentamicin. - Protein synthesis
tetracyclines inhibit:
protein synthesis
What do macrolides inhibit?
protein synthesis
give an example of a macrolide
erythromycin
What do lincosamides inhibit?
protein synthesis
Two lincosamides:
lincomycin and clindamycin
What do quinolones and floroquinolones inhibit?
DNA synthesis
Examples of Quinolones and fluoroquinolones:
naladixic acid, norfloxacin, and ciprofloxacin.
Random DNA synthesis inhibitors (not in their own class):
metronidazole and novobiocin
The RNA synthesis inhibitor:
Rifampin
What does Rifampin inhibit?
RNA synthesis
What class of drugs inhibit tetrahydrofolate biosynthesis? What are the examples?
Sulfa drugs
-trimethoprim and sulfonamides
Tetrahydrofolate-
an essential cofactor for
1-carbon transfer reactions (e.g., nucleic
acid synthesis).
Neisseria gonorrhoeae has an expressed pilin gene ______, which has a promoter. It also has 10-20 silent _____ gene copies, which lack promoters. Both have conserved and variable regions.
- pilE
- pilS
Recombination between the Neisseria gonorrhoeae pilin genes is called _________, not __________
- gene conversion
- homologous recombination
Natural transformation was originally demostrated by:
when?
Griffith in 1928
DNA picked up by natural transformation is integrated into the host genome via:
homologous recombination
Some bacterial species have specific receptors and will only take up DNA from the environment if it has ________
a recognized DUS (DNA uptake sequence)
Conjugation was first demonstrated in _____ by ________
- 1947
- Lederberg and Tatum.
Phage transduction was first demonstrated in ____ by _____.
He discovered the presence of ________ on a bacteriophage.
- 1951
- Freeman
- diptheria toxin gene
What are the two types of transducing phages?
generalized and specialized
Large chromosomal regions of horizontally acquired DNA:
GEIs (genomic islands)
What method is commonly used to identify genomic islands?
analysis of %G+C content along genome.
Genomic Islands
- They have a _____ content that differs from the rest of the genome.
- Derived from _____ or ______
- Usually associated with ______ in the chromosome (e.g., phage attachment sites, tRNA genes.
- G+C
- prophages; integrated conjugative elements.
- conserved sequences
Genomic islands
Flanked by _________.
A functional _______ gene is often present.
________ genes are sometimes present.
- repeat sequences.
- integrase
- Conjugation
When a genomic island contains one or more virulence genes it is known as a:
pathogenicity island (PAI).
What genes are typically found associated with genomic islands and pathogenicity islands?
Theoretically, any gene that increase fitness or versatility of bacteria is a candidate for HGT and therefore could end up in an island.
Examples of genes found in genomic islands and pathogenicity islands:
-Novel metabolic functions: ability to grow on novel carbohydrates.
- Xenobiotic resistance or utilization: pollutants
- Iron uptake systems
Antibiotic production.
- Symbiosis
- Antibiotic resistance genes
- Protein secretion systems, toxins
To survive in a host, a pathogenic bacterium
must do the following:
- Colonize host cells.
- Evade the host’s innate and adaptive immune
responses and thereby persist in the host.
3) Obtain essential nutrients such as iron which
may be limiting in the host. - Spread within a host and to other hosts.
Biofilms:
-Three-dimensional bacterial populations imbedded in an adhesive matrix (typically polysaccharide but may also contain protein or DNA) and attached to a surface.
Examples of medically related biofilms:
Examples: mucosal surfaces such as lungs
and wound sites, teeth (dental plaque), medical implants including catheters and plastic replacement parts (valves, hips, knees, etc.)
Biofilms:
- Show reduced susceptibility to _____
- Serve as a source for:
- antibiotics.
- bacteria to disseminate to other parts of the body.
what two properties facilitate colonization by allowing bacteria to reach mucosal surfaces?
motility and chemotaxis
Flagella-
long helical structures extending
out from the surface of the cell.
Most bacteria CANNOT survive without _____
iron
Iron is involved in many essential processes for bacteria, including: (3)
energy generation, DNA replication,
and protection from oxidative stress
Examples of host proteins bound to iron:
lactoferrin, transferrin, heme, ferritin
What can bacteria produce to acquire iron?
siderophores
Siderophores-
low molecular weight iron binding compounds
that have higher affinities for iron than the host proteins do.
Two examples of siderophores
entero-bactin from E. coli and anguibactin from Vibrio anguillarum
Pili-
Short proteinaceous rod-like structures
extending from the surface of cells and used
for attachment to surfaces.
pili are also called:
fimbriae
pilin are composed of:
of polymerized subunits of a single protein (pilin). Note: there are different types of pili that differ in their structures
surface adhesins that do not form
rod-like pilus structures are known as:
afimbrial adhesins (nonfimbrial adhesins).
Capsule-
Loose, relatively unstructured network of
polymers that covers the surface of a bacterium.
A capsule consists of:
polysaccharides usually, but other polymers have been discovered
Capsules protect bacteria from the host
immune system by reducing:
complement activation and opsonization.
Some bacteria evade host defenses by forcing their way into host cells. What is this called and how do they do it?
- bacterial mediated endocytosis
- inducing actin rearrangements similar to those of phagocytic cells ingesting bacteria
Bacterial mediated endocytosis
Surface proteins on surface of bacteria that cause this phagocytic response in non-phagocytic host cells are called:
invasins (internalins).
Name the four mechanisms that some bacteria have developed to survive phagocytosis:
- neutralize components of the phagolysosome
- resistance to oxygen radicals
- prevention of the phagolysosomal fusion event
- escape from the phagosome
How does a bacteria neutralize components of the phagolysosome?
alterations to the bacterial
cell membranes or LPS or to the presence
of a capsule.
How does a bacteria have resistance to oxygen radicals?
neutralizing them with various enzymes like catalase, superoxide dismutase, etc.
Give an example of a bacteria that can prevent the phagolysosomal fusion event?
Legionella pneumophila
How does a bacteria escape from the phagosome?
Escape is mediated by a toxin that targets the phagosomal membrane.
e.g. Listeriolysin O (LLO) of Listeria monocytogenes
Some bacteria can be taken up by non-
phagocytic cells, escape from the vacuole and then spread from cell to cell. This form of movement is known as:
Only 3 pathogenic species are
known to be capable of this:
- actin-based motility.
- Rickettsia rickettsii, Listeria monocytogenes, Shigella flexneri
Cell-to-cell spread:
For Listeria monocytogenes, a single surface
protein (____) polymerizes actin
filaments at one end of the cell. The resulting structure is called an:
- ActA
- actin tail (actin comet tail).
What type of bacterium is Helicobacter pylori?
Gram negative curved rod
Helicobacter pylori:
% of worlds pop. infected:
Symptoms range from _____ to _____
% of infected who get peptic and gastric ulcers:
% of infected who develop gastric cancer:
- 50%
- mild gastritis to peptic ulcers and gastric cancer
- 10%
- 1%
H. pylori is the first bacterial __________ declared by the WHO
class 1 carcinogen
What genes/proteins are found in all H. pylori strains?
What genes/proteins are additionally found in strains that cause gastric cancer?
- VacA, BabA, urease, Flagella
- Cag-PAI, CagA
What doe Cag-PAI encode?
a T4SS
Describe the pathway that leads to cancer by CagA:
CagA tyrosine residue (located on EPIYA motif(s) in the C-terminal) are phosphorylated by c-Src. Cag-A then interacts with and activates SHP-2. SHP-2 stimulates prolonged ERK kinase activity that leads to cell motility and cell elongation, which has been linked to cancer.
CagA causes the ______ phenotype in cells
hummingbird
