Metabolism VIII: reductive dehalogenation Flashcards
oxidation-state nomenclature
ASK HIM
For all the lectures where you said we should tailor it to our own interests would you say to just focus extra reading on those lectures only and then if we have time do more.
For section B on the exam do we have to show extra reading for this or is that more for section C
When we’re dealing with anions (negative ions) there are some conventions around naming:
highest oxidation state acid = …-ic acid sulfuric acid (H2SO4)
salt = …-ate sulfate (SO42-)
lower oxidation state acid = …-ous acid sulfurous acid (H2SO3)
salt = …-ite sulfite (SO32-)
semi-ionised forms with “H” are:
= hydrogen …ate/ite (HSO4- = hydrogen sulfate)
OR (interchangeable) = bi…ate/ite (HSO4- = bisulfate)
oxidation-state nomenclature
Sometimes, we get even higher and even lower options – usually less common!
highest-highest oxidation state acid = per-…-ic acid perchloric acid (HClO4)
salt = per-…-ate perchlorate (ClO4-)
next highest oxidation state acid = …-ic acid chloric acid (HClO3)
salt = …-ate chlorate (ClO3-)
next lowest oxidation state = …-ous acid chlorous acid
(HClO2)
salt = …-ite chlorite (ClO2-)
lowest-lowest oxidation state acid = hypo-…-ous acid hypochlorous acid (HClO)
salt = hypo-…-ite hypochlorite (ClO-)
overview
- oxidative dehalogenation is the oxidation of halocarbons as energy-and-carbon sources to form biomass/CO2
and halide ions (e.g. chloride, Cl-) with the halogen in the (-I) oxidation state in halides. At the expense of molecular oxygen as terminal electron acceptor. We aren’t going to cover this! - reductive dehalogenation is the reduction of halocarbons as terminal electron acceptors e.g. haloalkane respiration into alkanes and halide ions (e.g. chloride from chloroethane).
- (per)halate respiration is a special case of anaerobic
respiration: the use of halates and perhalates as terminal
electron acceptors. The elements are in the (V) and (VII)
oxidation states, respectively. Both are very strong oxidising
agents (better than nitrate, not as good as molecular
oxygen).
(same as nitric reduction but its an organic electron acceptor)
i.e. chlorate (ClO3-), perchlorate (ClO4-) (fireworks), iodate (IO3-), periodate (IO4-)
(per)halates in Nature
- (per)chlorate is found in Chile saltpeter (NaNO3)
deposits, particularly in the Atacama desert, Chile. - perchlorate probably forms in salt sprays owing to
photochemical oxidation of chloride ions but low levels. - nitrate fertilizers often contain low levels of perchlorate so it ends up widespread in soils but this is not natural occurrence!
- (per)bromate and (per)iodate are are not found in
Nature.
(easier to get nitrate than ammonia and less expensive)
halocarbons (Cl as EXAMPLE!)
- haloalkanes = C and H and halogen atoms. All single
bonds. - CCl4, carbon tetrachloride (tetrachloromethane)
- CHCl3, chloroform (trichloromethane)
- CH2Cl2, methylene chloride (dichloromethane)
- CH3Cl, methyl chloride (chloromethane)
- can also be mixed e.g. CH2ClF, Freon 31 (chlorofluoromethane) use it to freeze muscles or anesitice the skin
ethyls and higher would be cleaning stuff, solvents use in mass production of plastics - haloalkenes = same idea but double C=C bonds too.
- C2H3Cl, vinyl chloride (chloroethene) ??vinyles
- C2H2Cl2, vinylidene chloride (1,1-dichloroethene)
- C2H2Cl2, cis-1,2-dichloroethene and trans-1,2-dichloroethene
be careful with E/Z isomerism here - haloaromatics = contain benzene rings.
- C6H5Cl, phenyl chloride (chlorobenzene)
- C6H4Cl2, ortho-dichlorobenzene (1,2-dichlorobenzene)
- C6H4Cl2, meta-dichlorobenzene (1,3-dichlorobenzene)
- C6H4Cl2, para-dichlorobenzene (1,4-dichlorobenzene)
recalcitrant bacteria hasn’t evolved to degrade???
halogens in Nature
- halides are abundant in aqueous systems
- e.g. chloride in seawater, etc.
- halide minerals are abundant in Nature as
- e.g. halite aka rock salt (sodium chloride)
- e.g. fluorite aka fluorspar (calcium fluoride) – many types e.g. Blue John (too soft to carve so have a shine and impregnate with apoxy to harden them
- e.g. bromyrite aka bromargyrite (silver bromide)
- halomethanes are produced by many marine (bromomethane)made intentionally by marine groups such as Rhodophyta, Phaeophyta, Haptophyta etc quite
deliberately (all red); other haloalkanes are made in the same. Could be becasue they ar large prone to bacteria ???
Classes by the same enzymes: - bromide peroxidase (EC 1.11.1.18) which brominate
alkanes/alkenes/alcohols/etc e.g.
C6H14 + HBr + H2O2 → C6H13Br + 2H2O - chloride peroxidase (EC 1.11.1.10) which chlorinates
alkanes/alkenes/alcohols/etc
2 separate enzymes that can brominate or chlorinate
methanol is quite abundant in the upper oceans
Haloaromatics are also present in Nature: (halogens)
- e.g. vancomycin from Amycolatopsis orientalis from the
Pseudonocardiales of the Actinobacteria of the Actinomycetota of the Bacteria. Chloroaromatic. - e.g. thyroxine (“T4”) produced in the thyroid gland of the
Primates of the Animalia of the Eukarya, inc. Homo sapiens L. Iodoaromatic. - e.g. Tyrian purple is a bromoaromatic, namely 6,6′-
dibromoindigo. Produced by various marine Gastropoda e.g.
Bolinus brandaris L. and used since 400 BCE as a violet fabric dye. Nowadays used as a component of the pigment
MayaChrom Violet V2001F (PV58) sold as Mayan Violet as
a paint pigment (= Tyrian purple mixed with clays, metal
oxides and tree resin).
industrial use
- refrigerants (Freons/CFCs etc historically)
- propellants (ditto)
- solvents in industry and research and in dry cleaning
- plastic monomers
- e.g. vinyl chloride => polyvinyl chloride (PVC)
- e.g. vinylidine chloride => polyvinylidine chloride (PVDC)
- e.g. perfluoroethylene => polytetrafluoroethylene (PTFE aka Teflon)
- e.g. perfluoroethene + ethene => ethylenetetrafluoroethylene (ETFE aka Tefzel)
- e.g. chloroprene => neoprene
- halogenated natural rubber
- e.g. fluorine rubbers (FKM aka Viton)
- emulsifiers and surfactants
- e.g. brominated vegetable oil (BVO)
- e.g. perfluorocarbons
- flame retardants
- e.g. polybrominated diphenyl esters (PBDEs)
- inorganics:
- potassium (per)chlorate (weedkillers [now banned], explosives/fireworks/matches)
- ammonium (per)chlorate (rocket propellant)
reductive dehalogenation of haloalkenes
- tetrachloroethene reductive dehalogenase (EC 1.21.99.5) from Dehalobacter spp. (PceA, about 60 kDa):
many substrates e.g. cis-1,2-dichloroethene:
C2H2Cl2 + MKH2 → C2H3Cl + MK + H+ + Cl- the product
C2H2Cl2 (gets rid of halogen atoms to get into a stat that can be used more easily).(chloroethene) is then reduced by the same enzyme to ethene:
C2H3Cl + MKH2 → C2H4 + MK + H+ + Cl-
chloroethene easier to deal with.
only need specialist to remove some halogen atoms then generalists can do the rest to make it less recalcitrant.
- enzyme is corrinoid-dependent and uses menaquinol (MKH2) i.e. reduced quinone pool quinol as the electron donor, as such, this respiration doesn’t use bc1
complex et seq. if this is the only reaction. - useful in bioremediation as the more halogens on an organic molecule, the more recalcitrant it is and usually the more toxic too. Even removing just one halogen atom this way can make a big difference to oxidative dehalogenation rates.
- for haloalkAnes such as chloroform, there are other, partially characterised enzymes e.g. CfrA, CtrA, TmrA…these remove a Cl atom in the same way but in vivo electron donor unclear – maybe cytochrome c.
(per)halate respiration e.g. in Dechloromonas
- perchlorate reductase (EC 1.97.1.1, PcrABC) reduces perchlorate to chlorate, enzyme is PcrAB – PcrC is a cytochrome c that connects the enzyme to the quinone/ol
pool and PcrD is prob needed to assemble the Mo-cofactor:
ClO4- + QH2 → ClO3- + Q + H2O [also works for perbromate and periodate] - chlorate reductase (EC 1.97.1.1, ClrABCD) reduces chlorate to chlorite in same way as above:
ClO3- + QH2 → ClO2- + Q + H2O [also works for bromate and iodate] - chlorite-O2 lyase (aka chlorite dismutase (simultaneous oxidation and reduction), EC 1.13.11.49, Cld N.B. ‘dismutase’ is a misnomer – no dismutation happens!) reduces chlorite to chloride (non-toxic at low conc.) and molecular oxygen - this is a detoxification step and no electrons are transferred:
ClO2- → Cl- + O2 [no real evidence of working on bromite/iodite] need this in organisms otherwise the ies by it is not actually a respiratory enzyme.
This is specific to chlorite (ClO2- → Cl- + O2)
read Bender et al. (2005) J. Bacteriol. 187: 5090-5096.
