Cell barriers

Ethanol, benzene, toluene…

Soaps and detergents that destroy the plasmatic membrane of bacteria (our cells are protected by the croneum stratum)

Polyenes

Link to steroils, only for funghi

Polymixynes

Destabilizes the membrane because it has a hydrophobic tail that inserts in the membrane and forms channels. Low selectivity.

New lipopeptids (daptomycine)

Interact with the hydrophobic tails of the membrane and disipate the protonic gradient

Gramicidina

Example of antibiotic that forms channels for ions in the membrane

Charged antimicrobic peptides

Part of the innate inmune system, also destibilize the membrane of bacteria without interacting with ours because of the different charge.

N-actetyl-glucosammine

Derived from glucose, with an aminic group and an acetal group, and bound to NAM with b(1,4) linkage

N-acetyl-muramic

Derived from NAG (so also with an aminic group and an acetal group), with a lactic acid group bound by a eter linkage to four aa linked with peptidic linkage: L-alanine, acid D-glutamic, meso-diaminopilemic acid, D-alanine

Four aa in NAM

L-alanine, D-glutamic acid, mesodiaminopilemic acid, D-alanine

Link between two glicanic filaments (peptidoglican/muerin filaments)

Peptidic linkage between D-alanine and mesodiaminopilemic acid

Gram + bacteria different link between peptidoglican filaments

Peptidic linkage between D-alanine and lisine (instead of mesodiaminopilemic acid)

Teichoic acids

Polymers of glicerol or ribotol that contain phosphate. They increase the negative charge and strengthen the wall.

Lipoteichoic acids

Teichoic acids with a lipidic portion inserted in the membrane, anchoring the wall to the membrane

Teicuronic acid

A polymer of acetyl-glucosammine and glucoronic acid with no phosphate. Is an example of polisacharids in the wall that increase the negative charge and strengthen the wall.

Arabinogalactane layer

Layer of a polysacharide of arabinose and galactose which makes phosphodiester links with the peptidoglican layer. Found in micobacteria after the thin peptidoglican wall.

Micolic acids

Fatty acids with very lond chains that are part of an external membrane in micobateria. In this membrane we also find waxes, phospholipids and proteins

Lipo-arabino-manane (LAM)

Glicolipid found in the external membrane (made of micolic acids) of micobacteria. It is used in diagnostic tests and is very important in the infection process.

N-acetyl-talosaminuronic

Aminosugar found in the walls of archea, binds to NAG with a b(1,3) linkage and has 4 aa in the L form

four aas of the archae pseudopeptidoglicane

L-alanine, acid L-glutamic, L-linsine, L-alanine

Metanocondroitine

Protein similar to chondroitine present in archea forming an external protein layer.

MreB

protein that forms a structure similar to the cytoskeleton and controls the production of the peptidoglican wall

glicantentrapeptide

monomer of the peptidoglican (NAM+NAG+4aas)

UDP-NAG

Form of the NAG that enters the formation of the glicotetrapeptide because it saves energy in the phosphodiester linkage

MurA and MurB

Enzimes that transform UDP-NAM into UDP-NAG by transfering a latic acid group from phosphoenolpiruvate

MurC-D-E-F

Enzimes that add the 5 aas to the UDP-NAM (L-alanine, D-glutamic acid, mesodiaminopilemic acid, two D-alanines)

Bactenoprenol

Lipid made of 11 repetitions of isoprene (55C) and a P group. It binds to UDP-NAG with the release of UDP

Lipid I

Complex formed by bactenoprenol and NAG pentapeptide

Lipid II

Complex formed by bactenoprenol, NAG pentapeptide and NAM bound by a b(1,4) glicosilic linkage

MurJ

Flips the lipid II to the external face of the membrane, exposing the glicanpentapeptide to the exterior.

Transglicosilation

Pirophosphorilated bactenoprenol

Inactive bactenoprenol molecule left after transglicosilation, it needs to be in the monophosphorilated form to be active again

Penilining binding proteins

Membrane proteins responsible for the transglicosilation and transpeptidation in the formation of the peptidoglican wall. Link to penecilin.

Type A PBP

Responsible for the transglicosilation and transpeptidation

Type B PBP

Responsible for transpeptidation

Type C

Carboxipeptidase activity (they remove the terminal D-alanine) or endopeptidase activity (cutting of the internal peptide links

Elongases in peptidoglican formation

Needed to interrupt the continuity of the filaments and introduce new glicantetrapeptide units.

Cicloserina

Analog of D-alanine, it inhibits the racemase, the enzime that converts the L-alanine into D-alanine. Used for tuberculosis

Fosfomicina

PEP analog, which is a essential molecule for the formation of NAM, as it donates the lactic acid group

Bacitracina

Inhibits the dephosphorilation of bactenoprenol, which is an essential step to activate it, so the glicanpentapentide cannot be transfered to the membrane. Big polypeptide, so it is only efficient for gram+ bacteria

b-lactamic antibiotics

Inhibit the final stages of the peptidoglican synthesis, they interact with the PBP. They contain a b-lactamic ring structurally similar to the d-alanine dimer.

Peniciline

b-lactamic antibiotic, not for oral consumption because it is deactivated at low pH

Amoxicilline

semisynthetic penicilline, resistant to low pH but not to b-lactamases (resistance factor), so they need to be paired with inhibitors of b-lactamase

Cephalosporines of first generation

b-lactamic antibiotic only active for gram+ bacteria

Seconds generation cephalosporine

b-lactamic antibiotic also active for gram - bacteria, not toxic because the excess is excreted by urine

Three generation cephalosporine

b-lactamic antibiotic also active for gram - bacteria and able to pass the hematoencephalic barrier, so they can be used for encefalitis

Monobactamics

b-lactamic antibiotics used for very specific infections, they are very selective and respect the intestinal flora

Carbapenems

b-lactamic antibiotics with a wide action spectrum, used for infections againts bacteria resistant to other antibiotics

Vancomicina

glicopeptide antibiotic that inhibits tranglicolisation and transpeptidation because it binds to the glicantentrapeptide. It only works for gram+

Bacteriocine

Antibiotics produced by lactic bacteria, they are peptides that contain a lantionine aa

Nisina

bacteriocione antibiotic used as a conservant for food, it links to lipid II to inhibit peptidoglican synthesis. It also forms pores in the wall.

Lipid A

Hydrophobic part of the liposacarid that forms the external face of the outer membrane in diderms. Also called endotoxine.

LAL test

test that coagulates blood if the endotoxin (Lipid A) is present in the sample

Core of the LPS

sugary part of the LPS, formed by:

* the iner core: a proximal part formed by unusal sugars
* the outer core: a distal part formed by more common sugars

O-antigen

most external part of the LPS, it is antigenic so it generates immune response and memory. It is made of repetitions of a unit of 3-5 sugars.

type R LPS

LPS that only contains the lipid A, not the O-antigen or the core.

Braun lipoprotein

present in the external membrane, binds with the mesodiaminopilemic acid of the peptidoglican, anchoring the external membrane

MsbA

flip the lipid A-core complex from the inner part of the inner membrane towards the external face of the inner membrane

WaaL protein

links the O-antigen (that has been transported thanks to the bacterioprenol) to the lipid A-core complex already in the periplasm

Lpt complex

lypopolisacharide transport complex, a series of proteins in the inner m, outer m and periplasm that transport the LPS from the inner m to the outer m with ATP consumption

Bam complex

example of protein complex that is used to take proteins from the periplasm to the outer membrane

Sec pathway

General secretory pathway, a very conserved pathway involved in many forms of transport. It transports pre-proteins with a non-native configuration and a N-terminal signal sequence

SecB

A chaperone involved in the sec pathway, it is the most general one

SecYEG

Translocone in the sec pathway, formed by various transmembrane domains that form a channel. The transported protein is pushed by secA to get to the periplasm

SecA

protein that interacts with the translocone secYEG: it hydrolizes ATP and changes conformation, pushing the protein through the traslocone

N-terminal signal sequence (Sec pathway)

sequence formed by 3-8 basic residues, a hydrophobic core of 15-18 aas and 4-5 AlaXala residues preceding the cut site

Anchor peptide

N-terminal signal sequence for integral proteins of the membrane, it is very hydrophobic.

SRP-FtsY system

chaperon system used for the transport of integral proteins, the SRP is a ribonucleoproteic particle that acts as a chaperone, and it interacts with the signal sequence when the whole peptide is still being traduced by the ribosome. SRP interacts with FtsY, which takes the protein to the secYEG complex, where it be introduced in the membrane.

tat system

sec independent transport system, very important in archaea, transports folded proteins

type 1 systems

they are of the ABC transport systems (they have a membrane subunits with the ABC sequence that bind to ATP), sec indp

type 3 systems

needle-like systems, they inject substances in other cells. Very abbundant in pathogene bacteria, they are homologous to flagella (some subunits)

type 4 systems

homologous to pili, transport of protein and nucleic acids (TGO?)

type 6 systems

homologous to the contractile tails of bacteriophages, they inject toxines in other bacteria

type 5 systems

sec dependent transport system, the proteins have a b portion that, after they reach the periplasm, have autoproteasic functions. The b portion then forms a b barrel in the external membrane, letting the protein pass (usually toxins or adhesines)

type 2 systems

sec dependent systems, a very complex apparatus with ATPasic subunits.

Bacilli

Bastoncellare/rod shape

Cocchi

Sferical shape

Vibrioni

Spiral with one fold

Spirocheti

Spirals with various torsion points (very long)

Spirilli

Spirals with various folds

Pleomorph

Can change shape

Stafilococchi

Mass of cocchi associated

Bacteria that usually forms mycelliums

Actinobacteria

Phospholipids

Main components of the double layer that constitutes the plasmatic membrane in bacteria.

Diacil-glicerol-phosphate

A phospholipid, made of a glicerol head with a phosphate group, and two fatty acids bound by an ester link (COOH)

Opanoidi (opanoids)

Planar molecules that make the membrane more rigid in bacteria (instead of sterols)

What planar molecule do micoplasms have?

Sterols, because they take it from the host (they are obbligated parasites)

Phytanile

Fatty acids composed of branched isoprene chains. They bind to the L-glicerol with eter (CO) linkage, forming the phospholipids (dieter of phytanile) of the archea membrane.

Single layer membrane of archea

Formed by tetraeter of two molecules of glicerol and two long phytanile molecules (called diphytanile)

Rifampicina

Antibiotic with RNA polimerase as its target, only affects bacteria. Attacks the b subunit and inhibits the start of transcription.

Streptolidigina

Antibiotic that inhibits the start of transcription attacking the b subunit of RNA polimerase. Produced by Streptomyces, works for gram+ bacteria

sigma factors

transcription factors that allow the RNA polimerase to interact with the promoters, can be general (housekeeping genes) or specific (small groups of related genes)

nus factor

factors that associate to the RNApol in the enlongating phase and that have a limited proofreading capacity

rho

protein with atpasic and helicasic activity that participates in termination (which can be done with or withour rho)

CCR (Carbon Catabolite Represion)

Name of the system that inhibits the transcription of the lactose operon in the presence of glucose (EIIB phosphorilizes glucose instead of EIIA, so ac does not produce the coactivator, cAMP, and CAM/CRP is blocked)

Streptomycine/kanamicine

Aminoglicosid antibiotic that targets the 16S rRNA, making the ribosome “sloppy”, creating incorrect proteins

Puromycine

Aminoglicosid antibiotic that mimics the aminoacil-tRNA and causes the premature termination of traduction

Tetracline

polichetid antibiotic that links irreversibly to the 30S subunit of the ribosome, blocking the access to the A site

Macrolidi → eritromycine

polichetid bacteriostatic antibiotic that links to the 23S rRNA (P site) and bloccks translocation of the ribosome

Cloramphenicol

links to the 23S rRNA in the P site blocking the formation of the peptide link. Only used in the skin because it can be toxic for some organs

Oxazolidinone

for gram+, it links to the 23S rRNA and inhibits the initial complex of the traduction process