BLOCK 1 Dr. Robson Flashcards
What is the main difference between enveloped and non enveloped viruses ?
Non enveloped viruses are more resistant. Enveloped virus need an extra coat which is rich in glycoproteins to survive.
Virus with DNA genomes typically replicate where in the cell using DNA dependent DNA-polymerase of the host ?
Nucleus
RNA viruses can be positve sense or negative sense. Where does replication occur in case of RNA viruses ?
Cytoplasm.
Positive sense : comes already as a mRNA and can be translated.
Negative sense has to come preloaded with RNA dependent RNA-polymerse.
What do Toll-like-receptors bind ?
PAMPs
pathogen associated molecular patterns.
What specific PAMPs do TLR-2 and TLR-6 bind ?
LTA
Lipotheic acid (Gram +)
What specific PAMP binds to TLR-5?
Flagellin
Targets stuff outside the cell.
What specific PAMP does TLR-4 binds to?
Lipid A
Lipid A is found in the extra outer membrane of Gram - bact.
Target stuff outside the cell.
TLR-3 specifically binds ?
Double stranded RNA viruses
TLR-1 & 2 generally bind what ?
Bacterial lipoproteins (all bacteria) as well as mannose-conjugated proteins (all fungi)
Targets stuff outside the cell.
B-lactam atb target what?
Penicillin, Amoxicillin, Ampicillin, Ceftriaxone…
Transpeptidase enzyme
Builds the peptidoglycan layer forming alanine-alanine bridges.
Because the Lactam ring looks so similar to D alanine-alanine motif that is crosslinked, the enzyme actually binds the ring instead, which disables it. Cells can’t make normal cell walls.
Vancomycin & Daptomycin target what respectively ?
Vanco : Glycopeptide atb (targets alanine-alanine bridges)
Dapto : lipopetide atb (targets cell membrane)
IV rx (last resort for Gram + bacterial inx resistant to other meds)
What is polymyxin B ?
- Polymyxin B in the class of Colistin drugs
- Attack LPS (O-polysaccharide & Lipid A) , which are required for the bacteria to survive.
Super nephrotoxic. Usually used topically or as last resort.
What is Isoniazid used for ?
Trx of acid-fast bacterial infections.
Targets mycolic acid synthesis.
What is Pyrazinamide used for ?
Treats acid-fast bacterial infections by preventing interaction b/w mycolic acid cell wall and other cell layers, dirsupting aerobic respiration.
What is the advantage of making a capsule?
Made of polysaccharides that make them slippery. The aoid phagocytosis mainly this way. Also our immune system is bad at making response aginst CHO.
Gram + & Gram - can make a capsule.
What are biofilms?
Made by a dense population of bacteria. Comprised of CHO, lipids & proteins. Provide the same advantages as a capsule, plus resistance to antiseptics and atb.
What is type 3 secretion system ?
Especially used by gram - bacteria to inject protein that restructure actin filaments in host cells.
They use similar system than flagellum, pumping ATP via hollow tube.
4 steps of bacterial division:
- DNA replication resulting in 2 identical chromosomes
- As the cell elongates, chromosome segregate (they are attached to different parts of the membrane)
- Formation of septum by FTFZ ring that will divide the cell
- New cell wall and cell membrane completely divide the cell at the septum
These 4 steps represent the GENERATION TIME.
What is the generation time ?
time it takes for an initial population of bacteria to double
thicker and fancier the cell wall, the longer the generation time
Gram + longer than Gram - (more peptidoglycan layers)
- Acid fast bacteria is even longer (mycolic acid long +++)
Describe the bacterial growth curve.
Lag phase
Log phase
Stationnary phase
Decline phase
What are spores ?
Very very durable, non-metabolic state that a subset of gram + rods form to survive harsh conditions.
What class of bacteria causes infections in human bodies ?
Mesophiles.
What temperature range favorises these :
- a-helix structure
- î [unsaturated fats]
- î [AT] bases
Low temperatures.
What temperature range favorises these :
- b-sheets
- î [saturated fats]
- Î [CG] bases
Hot temperatures.
What enzyme neutralizes ROS ?
Catalase
What is the difference between obligate aerobes and obligate anaerobes?
Obligate aerobes : require O2 and are catalase-positive.
Obligate anaerobes: cannot tolerate O2 and are catalase negative.
Aerobes use oxidative phospho wheras anaerobes use fermentation.
What are facultative anaerobes?
Grow best with O2, but can also grow without. They are catalse-positive.
They use both oxidative phospho and fermentation.
Oxidative phospho is more efficient however, so favored.
What are aerotolerant anaerobes?
They tolerate, but do not use O2. They are catalse-positive.
Use fermentation.
They will just grow everywhere equally.
What are microaerophiles?
Use small amont of O2 to grow. They produce a small amount of catalse.
What is the mechanism of action of metronidazole?
drug reduced by ferredoxin (iron storage molecule)
Free rads obligate aerobes only can deal with that because they have a catalase enzyme.
Can be used against OBLIGATE ANAEROBES ONLY regardless if gram + or – .
Sulfa atb and trimethoprim disrupt what synthetic pathway in bacteria?
Folate synthesis.
Bacteria are RESISTANT if they can use EXOGENOUS FOLATE.
What is a nuclotid oligomerization domain (NOD)?
A type of protein that recognizes PAMPS in the cytoplasm of cells.
Specifically recognized peptidoglycan alanine bridges + NAMs.
Which type of bacteria has many layers of peptidoglycans (murein) making up their cell walls ?
Gram +
Why do Gram + bacteria stain purpule on gram-stain?
Thicker cell walls.
However, the peptidoglycan layer is the outermost layer making them more susceptible to b-lactam atb and lysosymes.
What atb are destroyed by b-lactamases?
First generation b-lactams
Penicillin, Amoxicillin, Ampicillin
An example of atb that is resistant to b-lactamases ?
New generation b-lactam such as Ceftriaxone
What are b-lactamases inhibitors ?
Chemicals that block b-lactamases, enabling the b-lactam atb to be effective even against bacteria that make b-lactamases.
Clavulanic acid ; bactams (sulbactam, monobactam, tazobactam)
What are Ziehl-Neelsen stains used for?
Acid-fast bacteria.
Pink means high mycolic acid contents and purple, means low mycolic acid content.
E.g. mycobacteria
What is capsule type switching?
Immunity against one capsule type (serotype) does not confer immunity against other capsule types.
What color do gram negative bacteria stain on gram-stain?
Pink
Staphlyoccoci tend to arrange as ?
Bunches
Like bunches of grapes.
Streptococci tend to arrange as ?
Chains
Like a peral necklace
What is the technique used to visualize spirochetes ?
Darkfield microscopy.
Because of their unusual morphology, they cannot be seen using gram-stains. Only EM or very specialized light microscopy techniques.
T or F. Both gram + and gram - can be motile ?
True
Flagella comprised of basal body attached to flagellin filament
Motility protein (mot) is attached to the ring of the basal body and harvests energy from proton falling down a proton gradient which spins the ring and in turn the flagellum. If it spins counterclock wise, in what direction does the bacteria travel?
Straight foward
If instead ATP is used instead of a proton gradient, the flagella will spin clockwise, which will result in incoherent spinning.
What are pili (fimbriae)
Flexible extensions through the cell envelope that can attach to somethinh with adhesin, then contract allowing them to move around.
Sex pili (not all bacteria) allow them to stick together & echange genetic material.
Why do spore-forming bacteria appear pinkish when all spore forming bacteria are really gram+ rods ?
They use their own peptidoglycans to make the additional layer between the 2 cell membranes.
Spores can’t be penetrated by gram-stain reagents so they appear as hollow holes on gram stained slide.
Malachite green/spore staining technique allows direct visualization of spores.
During wich phase of the growth curve do sporulation genes are expressed at the highest level ? Where would you see the most spores?
End of stationnary phase.
At end of decline phase.
(nb of bact at t=0)x(2^n)
allows you to calculate what?
The max nb of bacteria after a certain time.
What are capnophiles ?
They need a little bit of CO2 to grow (5-10%).
What types of bacteria are more likely to grow in the gut?
Facultative or strict anaerobe, mesophiles.
What type of bacteria is more likely to grown in the lungs?
Capnophiles, mesophiles.
What type of bacteria is more likely to grow in the upper respiratory tract, mouth?
Aerobic, mesophiles.
H2O2 would kill what types of bacteria ?
Anaerobes.
May invade puncture wounds (at bottom of wound, less O2)
Cellular respiration for generation of ATP occurs in the mitochondria of eukaryotes. Where does this process occur in prokaryotes ?
Plasma membrane.
Which byproduct of fermentation metabolism suggests that the bacteria uses fermentation to make ATP?
An acid of some kind.
They ferment CHO and make acid as a byproduct
What are a-hemolytic bacteria
Bacteria that can do partial lysis of RBCs on blood agar plates.
What are b-hemolytic bacteria ?
Bacteria that completely lyse RBCs on blood agar plates.
What are gamma hemolytic bacteria ?
Are not hemolytic at all. They do not break down RBCs on blood agar plate.
What is the use of blood agar plates?
ID bacteria who don’t, partially or fully break down RBCs.
Colonies growing right next to hemolytic bacteria on a blood-agar plates are called ?
Satellite colonies
They need blood to survive nut can’t break it down themselves.
Use chocolate-agar for these (contains RBCs that have already been lysed).
What are plasmids ?
Small circles of DNA that can be shared among bacteria. They usually contain the ‘‘Accessory genes’’ such as genes for atb resistance and virulence factors.
In the case of plasmid containing virulence factors, more copies of that plasmid = more copies of the virulence gene = more severe infections.
Genes that code for b-lactamase production are usually encoded on?
Plasmid
Atb resistance mechanisms that result from the mutation to the target enzyme itself (e.g. alternate transpeptidase) are usualled encoded where ?
Bacterial chromosome.
Bacterial chromosome encodes for the important stuff.
DNA topoisomerases II & IV which unwind the DNA upstream of the replication fork and allow decatanation of circular bacterial chromosomes at the end of cell divisions are targeted by what class of atb ?
Fluoroquinolones (Ciprofloxacin)
Incomplete cell division but disruption of DNA replication.
What is the concept of natural transformation?
Genetic exchange going on between live and dead bacteria.
Bits of DNA in the extracellular environment being taken up by a ‘‘competent cell’’ via ‘‘competent proteins’’ and being incorporated in the cell’s chromosome refers to what type of genetic material exchange?
Natural transformation.
What enzyme is required for natural transformation to occur and for fragmented DNA to successfully be incorporated into the cell’s chromosome ?
Recombinase coded for by recA.
What type of enzyme would interfere with natural transformation?
DNAse.
What is artificial transformation and an indication for it?
Involves researchers constructing a plasmid with a gene they want the bacterium to express, and forcing bacteria to take up the plasmid.
Indication : mass production of proteins (insulin).
Can be done with either gram + and gram -.
Conjugation is one way that bacteria have of sharing genes. What structure do they use to do so ?
Pili (flexible extensions through cell enveloped)
Classical conjugation is limited to Gram - bacteria
You need a flexible cell envelope which gram + and acid-fast bacteria don’t have.
Since conjugation can be interrupted by shaking, genes that are located where on the plasmid are more likely to be shared via conjugation?
Closest to the origine of replication.
What is a Hfr (high frequency of recombination) plasmid ?
A plasmid which has inverted repeat sequences that enables it to switch back and forth from being an independent plasmid to being integrated in a bacterial chromosome.
As part of the chromosome, the Hfr plasmid can’t be transferred via conjugation anymore, but when it pop’s back out, it may take a bit of the chromosome back out with it - what used to be a chromosomal gene is now in a plasmid and can now be transferred via conjugation.
What are bacteriophages ?
Viruses that can only infect bacteria by injecting DNA into their cell walls.
A phage that is only ever lytic is called ?
Virulent phage
Phages killing bacterial cells leave ‘‘plaques’’ wholes in an otherwise confluent layer of bacteria.
What is the CRISPR-Cas system ?
Bacterial immune system against phages.
Phages genome use palindromic repeats to integrate bacterial chromosomes.
- Phage DNA injected into bacterium
- Phage DNA cut by Cas proteins
- Palindrome fragment of phage DNA added to the library of phage DNA bits in the bacterial chromosome
- DNA that enters the bacterium in the future is compared to the CRISPR library and if it matches, its immediately destroyed.
The lysogenic cycle of bacteriophages refers to what?
All cells that can be lysogenic are called what?
Phage DNA is integrated into the bacterial chromosome, where it supresses all expression of lytic phase genes and does not harm the bacteria.
A phage that can be lysogenic is called temperate phage.
It just hangs out in the bacteria
Triggering of a temperate phage to switch from being lysogenic to lytic is called ?
Lysogenic induction.
Occurs when the bacteria replicate too fast or too stressed.
Unmethylated CG motifs in DNA of bacteria & viruses are recognized by what TLR?
TLR-9
Diphteria & Cholera toxins are disease-causing isolates of bacteria that are infected lysogenic phages containing virulence factors. Bacteria will express higher levels of phage virulent factor (lytic phages) at what phase of the growth curve ?
When bacteria are at highest population densities.
Generalized transduction is the result of what type of phages ?
Lytic phages
What is the difference between specialized and generalized transduction?
Generalized : Transferred any random of DNA that happen to be inside the parasitized bacterium and picked up accidentally by the lytic phage’s capsid.
Specialized : The location of the gene does influence the likeliness of the gene being transferred by the lysogenic phage.
DNA of donor needs to be alive in which genetic exchange mechanism?
Conjugation
DNA donor and recepients are closely related in what genetic exchange mechanisms ?
Conjugation
Transduction
Key mechanism that bacteria use to control their gene expression?
Production of different sigma factors under different environmental conditions.
Unwinding of DNA from histones prior to transcription is a key transcription regulator of ?
Eukaryotes
Genes that are expressed all the time (house keeping genes) are rich in ?
AT
Regulated genes, especially pathogenicity genes are rich in ?
CG
CG more difficult to separate strands and thus DNA harder to transcribe
What is an operon?
A set of genes that all get translated and transcribed at the same time.
what is quorum sensing ?
Quorum sensing is the regulation of gene expression in response to fluctuations in cell-population density. Quorum sensing bacteria produce and release chemical signal molecules called autoinducers that increase in concentration as a function of cell density. When autoinducer binds the receptor, second messagers are phosphorylated, new genes are transcribed and expression of genes is modified.
DNA sequences with what specific feature are more likely to be transposed ?
Palindromes (inverted repeats)
Rifampin disables what enzymes in prokaryotes but not in eukaryotes ?
RNA polymerase.
It binds the DNA where sigma would normally bind.
What is the only PAMP small enough to form a concentration gradient ?
AUG codon in prokaryotes (formyl-methionine)
Macrolides and tetracyclines inhibit protein synthesis by ?
Binding to bacterial ribosomes.
Tetracyclins (most cyclins) mechanism?
Bind to 30s sub-unit preventing small & large sub-units to interact thus stoping the initiation phase of translation.
Macrolides (end in mycins) bind to the 50s ribosomal unit (large) stoping what phase of translation?
Elongation phase
Name 2 exceptions ending with mycins that do not work by stopping the elongation phase of translation.
Vancomycin
Daptomycin
Dalfopristin-Quinupristin (synercid) mechanism of action and type of bacterial inx it treats?
combination of atb that binds different parts of of large sub-unit of ribosome (block elongation phase) for gram + severe infections resistant to other drugs.
IV administration
What are efflux pumps ?
Modifications of existing membrane proteins that pump atb out as soon as they diffuse into the cell. Allows resistance to atb with intracellular targets.
Possible in both gram + and -
What are heat shock sigma factors ?
EoH
Turn on genes that help the bacteria withstand environmental stress such as spore forming genes in spore forming bacteria.
What are siderophores?
Molecules secreted by bacteria to collect iron from the environment and transport it back into the cell.
