Metabolism VI: Fermentation ( read extra) rewatch Flashcards
overview on fermenting
- ferment from L. v. fermento, I rise, I leaven, I bubble, I
swell, I boil – this is owing to many (but not all) types of
fermentation resulting in gas emission. - no respiration occurs during fermentation.
- some fermenting organisms do have a respiratory chain
but only use it in reverse. They also have the ATP
synthase. They only use this if they have too much ATP,
so they can lyse it into ADP/Pi and generate Δp, which
then is used to make NAD(P)H – allows them to balance
ATP/NADH/NADPH/Δp (latter can be used for motility
etc). - don’t confuse with respiration of organic terminal
electron acceptors like fumarate! Kind of looks similar
as fumarate is reduced to succinate (and succinate IS
formed in some types of fermentation!). - many fermenters are aerotolerant anaerobes which will
grow under air (abundant O2!) but will ignore the O2
and ferment instead.
top fermenting yeast are aerotolerant
examples of bacterial fermentation
- sauerkraut production (Leuconostoc spp., lactic-acid Bacteria)
- gherkin production
- vinegar production (Acetobacter aceti*) (two version as real vinegar e.g malt but fake vinegar is chip shop vinegar
- fermented milk products (cheeses, yoghurts, (acidophiline)
many different organisms involved) - fermented fruits (atsara, burong mangga etc – similar organisms to sauerkraut)
- alcoholic drinks (beers, wines, amazake etc – mainly Fungi but Bacteria give flavour)
- pu’erh tea (Fungi plus Sphingomonas spp., Lactobacillus spp.)
- gimchi production (Bacillus spp., Lactobacillus spp., Serratia spp. etc)
[Mandarin v. 沉, to submerge; Mandarin pl. n. 菜 vegetables] - kombucha (昆布茶) production (Acetobacter spp. plus Fungi)
- dòufurǔ (tofu) (豆腐乳) production (mostly Fungi but some Leuconostoc)
- within Metazoa: vaginal fluid (lactic-acid Bacteria), gut contents (Enterobacteraceae).
vomit=mixed acid fermentation
revision – glycolytic pathways this is fermentation
what are the three pathways?
- also used for gluconeogenesis.
- all 3 used in Bacteria and Archaea – not all spp. have all of them, some use 1 only, some use all 3 at same time and balance them out.
- dissimilates sugars into pyruvate for trafficking into Krebs’ cycle via the link reaction.
Embden-Meyerhoff pathway (what Metazoa do):
glucose + 2NAD+ + 2ADP + 2Pi → 2 pyruvate + 2 NADH + 2ATP + 4H+
Entner-Doudoroff pathway (some Viridiplantae (poalese) use this, most use E-M):
glucose + NADP+ + NAD+ + ADP + Pi→ 2 pyruvate + NADH + NADPH + ATP + 2H+
pentose phosphate pathway (only Bacteria and Archaea) - the F6P/G3P then go into EM pathway:
glucose 6-phosphate + 2NADP→ 2 fructose 6-phosphate + glyceraldehyde 3-phosphate + 2NADPH + CO2 + H+
pentose phosphate pathway is sort of like an add on from the others.
some bacteria have more than one and so they acn inhibit enzyes to make????
More on fermentation
???substrate level phosphorylation
- all ATP is made during sugar dissimilation
- NAD(P)H is made during sugar dissimilation.
- the actual ‘fermentation add-on’ regenerates NAD+ only, and of course only does so if NADH is in excess in the cell.
- the sugar remains only partially oxidised: we don’t end up with every C becoming CO2 or biomass, stuff ends up as fatty acids, too.
- many types of fermentation (named for PRODUCTS!):
- ethanol fermentation (produces ethanol and CO2)
- lactic fermentations (produce lactic acid and sometimes other things)
- hydrogen fermentation (produces H2, acetate and bicarbonate)
- ABE fermentation (produces butan-1-ol, ethanol and acetone)
- mixed-acid fermentation (produces a mix of fatty acids)
(methanogenesis)
‘lactic acid bacteria’
Many changes of nomenclature and splitting of taxa over
the years. The bugs we are primarily concerned with are as
follows – N.B. genus Lactobacillus [L. gen. n. lactis, of
milk; L. masc. n. bacillus, a small rod; N.L. masc. n.
Lactobacillus, small rod of milk] was split in 2020 into 23
new genera. Overall homo/heterolactic types discovered
by Justus von Liebig
* Lentilactobacillus buchneri (homolactic), slow small rod of milk
- Loigolactobacillus bifermentans (heterolactic) ruin, destruction small rod of milk that destroys [can spoil products]; L. adv. bis, twice; L. masc. part. adj. fermentans,
leavening, bubbling, boiling; N.L. masc. part. adj. ferments in two parts,, spoils milk doubly fermenting] - Bifidobacterium bifidum (newer, unnamed lactic
fermentation!), a cleft small rod. Cells split
lactic fermentations: homolactic
done by some lactic-acid Bacteria e.g. Lentilactobacillus
buchneri.
NET: D-(+)-glucose + 2ADP + 2Pi → 2 lactate + 2ATP
Mainly done through EM pathway.
usually aerotolerant process (good for industry as excluding air is expensive)
L-lactate dehydrogenase (EC 1.1.1.27) recycles NADH
into NAD+ coupled to the reduction of pyruvate to lactate –
note the isomer.
pyruvate + NADH + H+ → NAD+ + L-lactate
D-lactate dehydrogenase (EC 1.1.1.28) does same but only
found in some specific species - note the isomer.
pyruvate + NADH + H+ → NAD+ + D-lactate
same reaction some species have either or both
* abundent acid produced – inhibits competing
organisms.
* relatively rapid metabolism of glucose to lactate.
* homolactic fermenters are generally aerotolerant
anaerobes.
EXAMPLES: most cheeses, yoghurt, vaginal fluid etc,
also note use of lactic acid in industry!
NO GAS PRODUCTION in homolactic production (one product)
lactic fermentations: heterolactic
done by some lactic-acid Bacteria e.g.Loigolactobacillus bifermentans.
NET: D-(+)-glucose + ADP + Pi → lactate + ethanol
+ CO2 + ATP
Enzymes same as previous – ultimately a combination
of ED and PP pathways used.
* abundant acid produced – inhibits competing
organisms.
* relatively rapid metabolism of glucose to lactate.
* heterolactic fermenters are generally aerotolerant anaerobes.
* Pentose phosphate pathway gives building-blocks for nucleic acid biosynthesis.
EXAMPLES: gut contents, ‘fizzy’ coleslaw, eyes in
Emmenthaler cheese…
This creates gas as CO2
lactic fermentations: the other one
done by Bifidobacterium bifidum.
NET: 2 D-(+)-glucose + 5ADP + 5Pi → 2 lactate + 3 acetate + 5ATP
Enzymes same as previous – ultimately a combination of ED and PP pathways used.
* not very well studied
* much higher ATP yield than other methods
EXAMPLES: some cheeses
look out for this NEW details
ABE fermentation
done by Clostridium acetobutylicum ‘the Wiezmann strain’ other Clostridium do it too. giving a 30/60/10 v/v/v ratio of acetone to butan-1-ol to ethanol [4.0/6.6/1.7 mol/mol/mol]
NET: D-(+)-glucose → ethanol + acetone + butan-1-ol +
acetate + butyrate
can’t balance reaction as many splits and depends on conditions
Very complex, branched pathway – makes it hard to
optimise industrially.
butan-1-ol shows great promise as a biofuel – can be added to petrol engines with no modification, alone, and they will run (cf. ethanol, which can only be used at 10 % v/v in petrol).
* getting pure butan-1-ol out is the challenge.
* widely used industrially to make acetone, wasting
the butan-1-ol.
butan-1-ol can make cars run
ethanol and butan-1-ol are very hard to separate a tey have very similar boiling and melting points. We can maybe make it from crop waste
read review by sauer don’t learnABE pathway
mixed-acid fermentation
done by Enterobacteraceae
good in colon not in stomach (food poisoning)
NET: D-(+)-glucose → succinate + lactate + formate* + ethanol + acetate
[* - some is broken down into CO2 + H2]
glucose → glucose 6-phosphate
some enters krebs cycle backwards (at the end)
glucose 6-phosphate → 2 phosphoenoelpyruvate (PEP)
PEP → oxaloacetate → malate → fumarate → succinate
PEP → 2 pyruvate
then pyruvate has two fates
pyruvate → lactate
pyruvate → formate → CO2/H2
pyruvate → acetyl-CoA (link reaction)
acetyl-CoA → acetaldehyde → ethanol
acetyl-CoA → acetyl phosphate → acetate
abundant acid production – pH drop is vast (this appears in the ‘methyl red test’ often used to distinguish Escherichia spp.)
common in upper GI tract
used in wine fermentation to add flavour complexity
low conc of succinate and lactate gives flavour compound on wine (not main flavour though)
Use textbooks
find examples for each fermentation, know which ones give which amounts of ATP and what are the benefits and negatives of each fermentation
