Week 1 Flashcards
Vibrio bacterial shape
comma shaped.
Spirochetes bacterial shape
flexible, spiral-shaped bacteria that have a unique, internal flagellar arrangement
How does surface area to volume ratio affect cell growth?
As this ratio increases, the uptake of nutrients and the diffusion of these and other molecules within the cell become more efficient, which in turn facilitates a rapid growth rate
Four components of phospholipids
Ethanolamine, phosphate, glycerol, fatty acids.
Hopanoids
sterol-like molecules found in many bacterial plasma membranes. synthesized from the same precursors as steroids, and like the sterols in eukaryotic membranes, they probably stabilize the membrane
Three types of growth factors for bacteria
amino acids, purines and pyrimidines, and vitamins
Types of substances that can move across the plasma membrane via passive diffusion
O2, CO2, and water.
Three types of active transport observed in bacteria
primary active transport, secondary active transport, and group translocation
ABC transporters
ATP-binding cassette transporters, important primary active transporters
MFS transporters
Secondary active transporters include the major facilitator superfamily (MFS) proteins. MFS transporters use ion gradients, some of which are created by bacteria during their metabolic processes
distinguishing characteristic of group translocation
a molecule is chemically modified as it is
brought into the cell
PTS transport
phosphoenolpyruvate: sugar phosphotransferase system, which transports a variety of sugars while phosphorylating them, using phosphoenolpyruvate (PEP) as the phosphate donor.
siderophores
low molecular weight organic mole cules that bind ferric iron and supply it to the cell
periplasmic space
a space between the plasma membrane and the outer mem brane. It also is sometimes observed between the plasma membrane and cell wall in typical Gram-positive bacteria.
Which amino acids can be found in peptidoglycan, and what is their function?
Three of the amino acids are not found in proteins: o-glutamic acid, D-alanine, and meso-diaminopimelic acid. The presence of D-amino acids protects against degradation by most peptidases, which recognize only the L-isomers of amino acid residues
Two phyla that most gram positive bacteria belong to
Most bacteria that stain Gram positive belong to the phyla Firmicutes and Actinobacteria
Teichoic acids
polymers of glycerol or ribitol joined by phosphate groups, often covalently connected to peptidoglycan or to plasma membrane lipids. Contribute to the negative charge of bacterial cell wall.
Braun’s lipoprotein
the most abundant protein in the outer membrane, links the outermembrane to the underlying peptidoglycan cell wall;.
Three components of LPS
(1) lipid A, (2) the core polysaccharide, and (3) the 0 side chain.
lipid A region of LPS
contains two glucosamine sugar derivatives, each with three fatty acids and phosphate or pyrophosphate attached. The fatty acids of lipid A are embedded in the outer membrane, while the remainder of the LPS molecule projects from the surface
Core polysaccharide of LPS
joined to lipid A and is constructed of 10 sugars, many of them unusual in structure.
O antigen or side chain of LPS
a polysaccharide chain extend ing outward from the core. It has several peculiar sugars and varies in composition between bacterial strains
Functions of LPS in bacterial outer membranes
(1) It contributes to the negative charge on the bacterial surface because the core polysaccharide usually contains charged sugars and phosphate (figure 3.26). (2) It helps stabilize outer membrane structure because lipid A is a major constituent of the exterior leaflet of the outer membrane. (3) It helps create a permeability barrier.
Three best-studied cytoskeletal elements of bacteria
FtsZ, MreB, and CreS
FtsZ
one of the first bacterial cytoskeletal proteins identified and has since been found in most bacteria. FtsZ is a homologue of the eukaryotic protein tubulin. It forms a ring at the center of a dividing cell and is required for the formation of the septum that will separate the daughter cells
MreB
actin homologue. major function is to determine cell shape in rod-shaped cells; MreB is not found in cocci. MreB and Mbl determine cell shape by properly positioning the machin ery needed for peptidoglycan synthesis
CreS
was discovered in C. crescentus and is responsible for its curved shape (figure 3.32d). CreS is a homologue of lamin and keratin.
polyhydroxyalkonate (PHA)
How carbon is stored in storage inclusions in bacteria.
carbonic anhydrase
converts carbonic acid into C02
MIC
minimum inhibitory concentration
Legionella pneumophila characteristics
a nutritionally fastidious, aerobic, Gram-negative rod
Thus the catabolism of glucose to pyruvate can be represented by this equation.
Glucose+ 2ADP+ 2P;+ 2NAD+ ->
2 pyruvate+ 2ATP + 2NADH+ 2H+
One-step secretion systems that can span two membranes in Gram-negative bacteria
Secretion system Types I, III, IV, VI, and VII
What is required for protein secretion by gram-negative bacteria that do not have a secretion system type that allows for secretion through both membranes?
A common Sec/TAT pathway which will export the product into the periplasmic space. These products will then be further secreted by type II, V or IX secretion systems
Differences between the Sec and TAT translocaes complexes
Sec translocase complex will export unfolded proteins into the periplam. If proteins require cytoplasmic folding before secretion, the TAT complex is required.
Type of secretion system in M tb.
Type VII secretion system, ESX-1
Only known Mtb exotoxin
C-terminal domain of the outer membrane protein CpnT, named TNT
Are Archea more closely related evolutionarily to Eukaryotes or Prokaryotes?
Eukaryotes
What are the only known bacteria to not have cell wall?
Mycoplasma
What are 5 different types of plasmids that can occur in bacteria?
Conjugative plasmids that aid in DNA exchange between individuals (example is F factor)
R plasmids - contain resistance cassettes
Col plasmids - toxin production
Virulence plasmids
metabolic plasmids
Who developed Gram stain and in what year?
Hans Christian Gram, 1844
What are the individual steps for a Gram stain?
Add Crystal Violet
Add Iodine
Decolorization with acetone/alcohol (wash)
Add Safranin
What are some of the modern uses for determining Gram staining?
Treatment of infection in the ER - antibiotics for Gram negative and Gram-positive bacteria are often very different; this simple stain can help physicians choose treatment options quickly
What are some major differences between mitosis and binary fission?
- Replicated DNA attaches to spindle apparatus in mitosis; cell membrane in binary fission
- DNA replication and division are separate events in mitosis; they happen concurrently in binary fission.
- Binary fission is more error-prone than mitosis.
What is the advantage of asymmetrical cell division in mycobacteria?
The parent cell can ‘offload’ misfolded and oxidized proteins into the smaller of the two daughter cells, improving the fitness of the other daughter cell.
What are the requirements for Sec translocon peptide secretion?
ATP and proton motive force. Peptides require a signal peptide. Can only transport unfolded peptides.
What are the requirements for Twin-arginine translocation (TAT) secretion system?
Transports folded and unfolded proteins, a well as larger protein complexes that may contain cofactors. Only requires the proton motive force (no ATP). Signal peptide is required: twin-arginine motif.
What is unique about the type III secretion systems?
They span three membranes - the inner and outer membrane of the bacteria, as well as the cel membrane of the host, to ‘inject’ effector molecules.
Examples of Yersinia enterocolitica effectors
YopJ - cysteine protease, prevents activation of MAPK and NFkB
YopE - inhibits Rho GTPases (disruption of actin filaments)
YopH - tyrosine phosphatase, dephosphorylates key actin cytoskeletal proteins, inhibits Ca2+ signaling.
Altogether, these suppress phagocytosis.
Are mycobacteria gram positive or gram negative?
Neither. They have features of both, including an inner and outer membrane (a la Gram Neg) and a thick peptidoglycan layer (a la Gram positive). They have also. a thick waxy outer coating that prevents proper Gram staining of their peptidoglycan.
Divisome
Protein complex coordinating the binary fission of bacteria, formed under the direction of the Z ring.
FtsZ
Conserved tubulin homologue in bacteria that polymerizes to form the Z ring, essential for bacterial binary fission.
Membrane targeting sequence
Protein complex that tethers FtsZ to the inner cell membrane to begin forming a proto-ring for binary fission. In E coli, this consists of FtsZ, FtsA, and ZipA
How is mycobacteria cell division different from traditional binary fission?
Mycobacteria undergo asymmetric cell division, and grow at the poles of the two proto-daughter cells, rather than at the center of the cell during elongation.
What is one way to recognize pathogeniciity islands in bacterial chromosomes?
They often have a different G:C content from the rest of the chromosome, due to horizontal gene transfer.
SPI1
Salmonella Pathogenicity Island 1 - 40kb region encoding T3SS, proteins secreted by T3SS, chaperones and regulatory proteins
HPI
High pathogenicity island on chromosomes of pathogenic Yersinia strains, encodes genes involved in biosynthesis, transport and regulation of the siderophore yersiniabactin, i.e. major function of this island is for in vivo bacterial growth and dissemination.
Three methods of horizontal gene transfer
Transduction (via bacteriophage)
Conjugation (direct contact)
Transformation (Uptake of free DNA or plasmids)
What are some methods of antibiotic resistance?
Target modification (target replacement, target mutation, enzymatic modification of target, or target protection)
Decreasing concentration of antibiotic inside bacteria (efflux pumps or blocked entry of antibiotic)
Degradation or altering of the antibiotic by enzymes.
Koch’s postulates (quote)
“To prove that TB is caused by the invasion of bacilli, and that it is a parasitic disease primarily caused by growth and multiplication of bacilli, it is necessary to isolate the bacilli from the body, to grow th m in pure culture until they are freed from every disease product of the animal organism, and, by introducing isolated bacilli into animals, to reproduce the same morbid condition that is known to follow from inoculation with spontaneously developed TB material”
Koch’s postulates and problems with each (list)
I. Association of the microbe with the lesions of the disease (Problem - some bacteria colonize without causing symptomatic disease)
II. Isolating the microbe in pure culture (Problem - some bacteria cannot be cultivated)
III. Showing that the isolated microbe causes disease in humans or animals (Disease too serious for humans, and perhaps no animal model exists)
VI. Reisolating the microbe from the infected animal (probably no problem here)
What is the proposed fifth postulate for Koch’s postulates?
Information about microbe should enable scientists to design effective therapeutic or preventative measures
Varieties of host-microbe interactions
- Susceptibility and host response: not all individuals are equal in their response to a pathogen (immunocompetent vs imunocompromised)
- Pathogenicity - not all strains of a microbial species have equal ability to cause disease
Views of host-microbe interactions
- Disease causing bacteria evolved specifically to cause human disease (thy’re out to get you)
- Disease symptoms result when equilibrium ddoes not develop between disease-causing microbes and host
- Humans as accidental hosts of microbes that normally occupy another niche (they’re lost and not happy about it)
True virulence genes
Genes encoding for factors or enzymes producing factors that are:
- involved in interactions with the host AND
- directly responsible for the pathological damage during infection AND
- absent in apathogens.
Virulence-assocaited genes
Genes encoding for factors or enzymes producing factors that:
- Regulate expression of virulence genes OR
- activate virulence factors by translational modification, processing or secretion OR
- are required for the activity of the true virulence genes
Virulence life-style genes
Genes encoding for factors or enzymes producing factors that:
- enable colonization of the host OR
- enable evasion of the host immune system OR
- enable intracellular survival OR
- employ host-factors for benefit of survival
How do bacteria use biofilm formation?
Bind to surfacesk establish multilayered communities, reduced susceptibility to antibiotics, bacteria continue to dislodge and disseminate throughout body
How do bacteria use motility and chemotaxis?
For reaching mucosal surfaces (especially areas with fast flow or with nutrients)
How do baceria use siderophores?
For iron acqquiisiton
Pathogenicity factors of extracellular bacteria
Localized inflammatory response (EPEC), toxin production, exotoxins (cholera), and endotoxins (E. coli)
Main immune response is humoral - antibodies, complement and phagocytosis
What are some bacterial defenses against humoral immunity?
Expression of poorly antigenic antigens
- Antigenic variation
- Antigenic mimicry
- Expression of antibody-cleaving proteases
- -Expressio n of antibody-binding molecules
Opa/Opc proteins
hypervariable surface antigens expressed by N. gonorrhoeae, to evade humoral immunity. Can also switch off pilus expression.
Slipped strand mispariing
Through either transcripitonal or translational control, mecahnistically allows gene expression at the protein level to be modified for antigenic variation
Bacterial defenses against cell-mediated immunity
Inhibition of phagocytosis
- Inhibition of phagosome-lysosome fusion
- Suppression of cellular responses/cytokine production
- Block antimicrbial molecules
- Escape from the phagosome
How does Mtb prevent phagosome-lysosome fusion?
Through factors secreted by the T7SS, damages phagosomal membrane integrity, which leads to the prevention of ATPase and NADPH oxidase recruitment
Ways that T3SS effector proteins modulate host cell activity
Induction or prevention of pahgocytosis through cytoskeletal modifications
Modifications of cellular trafficking to allow for replication within or escape from phagosomes
Inhibition of inflammasome activation
Modulation of NfkB and MAPK signaling pathways to downregulate inflammatory cyotkines
What is the ‘outer capsule’ of mycobacteria composed of?
esterified mycolic acids (long (~90 carbons) fatty acids) that are either covalently attached to peptidoglycan or hydrophobically assocaited. Those mycolic acids that are hydrophobically assocaited are often virulence factors or inflammatory mediators.
What are the advantages that the ‘outer capsule’ confers upon mycobacteria?
It is extremely hydrophobic, thus drugs to not easily penetrate through the outer capsule.
What is the general chemistry of fatty acid synthesis?
Repetitive condensation of two-carbon units (acetyl CoA) onto a growing lipid chain.
What are the differences in enzymes for fatty acid synthesis between eukaryotes, bacteria, and mycobacteria?
Eukaryotes utilize Fatty Acid Synthase I, which is a multimeric enzyme.
Bacteria utilize a Fatty Acid Synthase II, which are individually encoded proteins that each carry out the four reactions.
Mycobacteria have both FAS1 and FAS2, each of which is responsible for a different portion of the FA chain (FAS1 makes alpha branch, FAS2 makes the long, main chain) These chains are synthesized separately and joined together by PKS13, an essential enzyme for mycobacteria
Types of tests for TB:
TB skin test (TST) - s.c. antigen exposure, looking for delayed hypersensitivity T cell reaction within 48h
IGRA - IFNg Release Assay - using antigenic peptides derived from pathogenic TB (and absent in BCG; esxA and esxB) to activate isolated T cells from patients - this works around the fact that BCG-vaccinated people will often test positive for skin tests.
How common is reactivation of latent TB?
10-15%, most within the first 5 years after exposure.
Three modes of signal transduction in mycobacteria
- Two component systems
- Serine-Threonine kinases
- Proteolytic signal transduction
