Antibiotics Flashcards

Question

It what form is folate used

Answer 1

Hydrogenated to dihydro-folic acid or tetrahydro-folic acid

Answer 2

Sulfonamides

Answer 3

p-aminobenzoic acid (pABA)

Answer 4

Synthesis of purines Synthesis of thymine by methylation of dUMP

Answer 5

Dihydrofolate reductase

Answer 6

Catalyse the passage of a single stranded molecule through a single stranded gap

Answer 7

Catalyse the passage of a double stranded molecule through a double-stranded gap

Answer 8

Catalyses transient breakage of DNA Catalyse strand passage Removal of supercoils and torsional stresses to allow the replication fork to continue

Answer 9

between an enzyme tyrosyl and a DNA phosphate group leads to the breakage of a DNA backbone bond and the formation of a covalent enzyme–DNA intermediate. Rejoining of the DNA backbone bond occurs by the reversal of the reaction shown. In the reaction that is catalysed by a type IA or a type II enzyme, a 3′-OH is the leaving group and the active-site tyrosyl becomes covalently linked to a 5′-phosphoryl group, as depicted. In the reaction that is catalysed by a type IB enzyme, a 5′-OH is the leaving group and the active-site tyrosyl becomes covalently linked to a 3′-phosphoryl group.

Answer 10

Portion of DNA that transverses the temporary gap

Answer 11

Portion of DNA with the gap

Answer 12

ATP and ARP hydrolase

Answer 13

Type 2 topoisomerase Removes torsional stresses in prokaryotic dna

Answer 14

Topoisomerase in eukaryotic cells The enzyme catalytic tyrosine is linked to the phosphate group on the 3’ end of the DNA; the 5’ OH is free. This is the topoisomerase activity that supports the removal of torsional stress in eukaryotes. Rotates the dna to relax the supercoiling

Answer 15

The binding site overlaps with that of the ATP, which explains the competitive inhibitor nature of the drug

Answer 16

Novobiocin Fluoroquinolone

Answer 17

Interferes with ATP binding to GryB

Answer 18

mild diarrhea (37 per cent), skin rashes (8.9 per cent), fever (2 per cent), eosinophilia (high eosinophil count [500+/μl]; 1.47 per cent), gastrointestinal irritation with nausea (1.3 per cent) leukopenia (low white blood cell count; 0.6 per cent) yellowish discoloration of the skin and sclerae occasionally (0.6 per cent). The pigment is believed to be a degradation product of the drug and not related to hepatic dysfunction.

Answer 19

Eukaryotes also have type 2 topoisomerase

Answer 20

Bind to cleft between 2 subunits of topoisomerase - site of action for the enzyme Prevents religation of broken DNA Topoisomerase remains forever due to covalent bonds with broken DNA - permanent

Answer 21

may be damaging the mitochondria – a historical effect of the bacterial origin of mitochondria. But they don’t have type II topoisomerase in them! It may be causing oxidative stress There is also data that specific gene variants in sick people influence the metabolism of the drug and hence it may be toxic in these people

Answer 22

4 subunits 1 regulatory sigma subunit

Answer 23

Ansamycins — Rifampicin

Answer 24

It doesn’t affect promoter binding Binding of the 1st nucleotide is unaffected So is the making of the 1st phosphodiester bond, that is the 1st dinucleotide It is at the stage of forming the 2nd or the 3rd phosphodiester bond when the inhibition kicks in Furthermore, when RIF is added once the RNAP engaged in processive RNA synthesis – elongation, it was also ineffective the antibiotic does not interfere with substrate binding, catalytic activity, or the intrinsic translocation mechanism of the RNAP

Answer 25

RIF binds to exit pore of the rna polymerase so the growing RNA chain so that it cannot exit via the exit pore

Answer 26

Anti cancer drug Binds to DNA - intercalates between the bases Forms hydrogen bonds with the molecule

Answer 27

RNA polymerase I

Answer 28

Synthesises rRNA

Answer 29

block initiation Oxazolidinones block elongation macrolides such as lincosamide and streptogramin

Answer 30

block AA-tRNA entry to the A site tetracylines streptomycin spectinomycin aminoglycosides

Answer 31

Bactericidal

Answer 32

Mainly active against Gram positives and Mycoplasmas It ‘plugs’ the peptidyl exit tunnel on the ribosome L-cladinose: a methylated hexose ring 1st and 2nd generation macrolides are considered safe and well tolerated. Some 3rd generation ones exhibit hepatotoxicity

Answer 33

positively charged and attach to the negatively charged lipopolysaccharides on the outer membrane of Gram negative bacteria. This binding opens the outer membrane For passing the inner membrane it uses active bacterial transport mechanisms that are oxygen dependent. Consequently, aminoglycosides don’t work in anaerobs.

Answer 34

Freezing in the ON state permits the binding of other non-matching AA-tRNA molecules to the A site This will lead to misreading of the mRNA and a garbled protein Some aminoglycosides (spectinomycin and hygromycin, for example) also influence dynamic changes associated with translocation Streptomycin has a different binding site and interferes with the initial AA-tRNA selection

Answer 35

TETs travel through the outer membrane through OmpF and OmpC porin channels of Gram-negative bacteria complexed with a Me++ In the periplasm they dissociate and the TET molecule diffuses through the inner membrane Gram-positive uptake is similar (except passing the outer membrane, of course) Inside they are likely complexed with Me++ again They bind to the A site and interfere with AA-tRNA binding

Answer 36

Binding of the tRNA to the A site is a two-step event. The tRNA initially binds in the OFF state in a fast equilibrium reaction. Docking of the correct tRNA causes the flip to the ON state, which induces other conformational changes in the ribosome to induce a precise fit.

Answer 37

Designed to treat the bacterium Treponema pallidum The compound atoxyl was an arsenic derived derivative that Ehrlich realised was too toxic, but that it contained an active ingredient, arsenic. He worked with synthetic chemists to create organo- arsenic compounds and came up with salvarsan. But actually, they didn’t fully understand the structure.

Answer 38

Target identification and validation Assay development Virtual screening (VS) High throughput screening (HTS) Quantitative structure – activity relationship (QSAR) and refinement of compounds Characterisation of prospective drugs Testing on animals for activity and side- effects Clinical trials Licensing approval

Answer 39

The peptidoglycan precursors are synthesized into lipid II in the cytoplasm. This is “flipped” across the membrane by the transport lipid (undecaprenyl phosphate). The glycosyltransferase (GT51) catalyses polymerization of the nascent peptidoglycan chain from lipid II. Vancomycin and teicoplanin bind to the terminal D-alanyl-D-alanine moieties of the NAM/NAG-peptides preventing peptidoglycan formation. Nisin and teixobactin interact with the pyrophosphate of lipid II Bacitracin affects the phosphorylation of C55-isoprenyl pyrophosphate and related bactoprenol pyrophosphate by binding to the pyrophosphate of these molecules.

Answer 40

1. Penicillin scaffold. 2. Cephalosporin scaffold. 3. (1-methyl) Carbapenem scaffold.

Answer 41

The ED50 (median effective dose) is the dose of a medication that produces a specific effect in 50% of the population that takes that dose The median toxic dose is the dose required to produce a defined toxic effect in 50% of subjects; The median lethal dose is the dose required to kill

Answer 42

Collection of environmental sample Plate out to culture diverse community Isolation of pire microorganisms for screening Liquid culture Extracts on disks

Answer 43

Re screen fraction Identification of active compound - mass spectrometry/ NMR Consider producing synthetically Mode of action

Answer 44

Inhibitory Concentration is the lowest drug concentration that prevents visible microorganism growth after overnight incubation. The concentration normally given in µg/ml MIC tests are carried out in 96 well plates Tests are normally carried out in triplicate The concentration of antibiotic is diluted by half in each well across the plate Well 12 contains no antibiotic (control) The concentration starts at 256μg/ml Test again a number of strains (ESKAPE pathogens)

Answer 45

Consider toxicity testing

Answer 46

Galleria mellonella (Wax moth Larvae) are used to study bacterial infections and antibiotic activity. They mimic the mammalian innate immune system so make a good substitute for mammalian models. They are easy to maintain and are low cost They don’t require the same ethical approval as vertebrate models Testing is easy to carry out, no specialist training is required

Answer 47

quantitative measure that indicates how much of a particular inhibitory substance (e.g. drug) is needed to inhibit, in vitro.