Phys Exam 2

Front 1

Clostridial fermentation calculations

Back 1

1. How many H2 from NADH reox?

(rest are from Fd reox)

2. Will use 2 NADH per Glu.

3. 2*(Glu)-(Number reox)= NADH left to reox

4. Must make 1 butyrate for every 2 NADH reox.

5. Will use 2x as many Acetyl-CoA (out of 2x glucose) to make but.

6. Rest of acetyl CoA will make 1x acetate

7. ATP: 2x glucose (EMP), 1x but, 1x acetate

Front 2

Reactions that make NADH and FDred

Back 2

C: pyruvate + CoA + FDox ->CO2 + acetylCoA + FDred

P: pyruvate + CoA + NAD+ ->CO2 + acetylCoA + NADH + H+

Both: glyceraldehyde3P + NAD+ -> 1,3bisPglycerate + NADH + H+

Front 3

Reactions that make NAD+ and FDox

Back 3

C: crotonyl-CoA + NADH + H+ -> butyryl-CoA + NAD+

acetoacetyl-CoA + NADH + H+ -> 3-hydroxybutyryl-CoA + NAD+

P: oxaloacetate + NADH + H+ -> malate + NAD+

fumarate + NADH + H+ -> succinate + NAD+

Front 4

Reactions that make ATP

Back 4

C: butyrylP + ADP -> butyrate + ATP

Both: phosphoenolpyruvate + ADP -> pyruvate + ATP

1,3bisPglycerate + ADP -> 3Pglycerate + ATP

acetylP + ADP -> acetate + ATP

Front 5

Back 5

5' deoxyadenosyl-cobalamin (B12)

Fxn: H rearrangement

forms a free radical used to remove H from substrate

Front 6

What cofactor is involved in this reaction?

Back 6

5'-deoxyadenosyl-cobalamin (B12)

Front 7

Back 7

biotin

Fxn: transcarboxylation, carboxylation/decarboxylation

Front 8

What cofactor is involved in this reaction?

Back 8

biotin

Front 9

Back 9

5,6,7,8-tetrahydrofolate (folic acid/para-aminobenzoic acid)

Fxn: one carbon transfer (NOT carboxy transfer)

used by acetogens to form methyl group of acetate

Front 10

function of ferredoxin

Back 10

electron transfer

Front 11

enzymes used to metabolize pyruvate

Back 11

pyruvate:ferredoxin oxoreductase

pyruvate formate lyase (enterics)

Front 12

metals besides Fe used by hydrogenases

Back 12

Ni, Se

Front 13

why is ATP needed to fix N2

Back 13

to lower redox potential of electrons transferred to nitrogenase

Front 14

how do pyruvate-formate lyase and methylmalonyl-CoA mutase cleave C-C bonds

Back 14

free radical

Front 15

what mods to iron in Fe-Fe hydrogenases allow them to make H2

Back 15

CO or CN bound to Fe

Front 16

main functions of methanogens

Back 16

hydrogen and acetate use

Front 17

why is T. maritima's hydrogenase able to produce H2 from NADH AND FDred (a lot of H2)

Back 17

coupled reactions; production of H2 from FD is favorable, used to drive H2 production from NADH which is unfavorable

Front 18

why is it difficult to make 12 H2 from glucose

Back 18

reactions that take hydrogen from acetate, butyrate, propionate (intermediates in anaerobic degradation of glucose) are endergonic (unfavorable thermodynamically)

Front 19

fxn of MoFe protein in N2 fixation

Back 19

reduces N2 to 2 ammonia (NH3)

Front 20

would G- bact that fermented glucose and made 2,3-butanediol be a health risk?

Back 20

no, 2,3-butanediol indicates bact from plants not fecal matter

Front 21

why is colon fermentation good for your health/ why would switching from red meat to grains help colitis

Back 21

butyrate is important for epithelial cell devop., colon cancer/colitis, immune system control. enterics will turn meat into toxic H2S in small intestine, but grains/veggies have nonreactive starch that will make it to large intestine and get fermented to acetate, propionate, butyrate

Front 22

why would a digestor run at fast retention times cause acetate, propionate, and butyrate to accumulate

why would BESA cause this

Back 22

too fast for acetate-using methanogens and syntrophic metabolizers to grow. H2-using methanogens grow faster so high H2 pp is not problem

methanogens are inhibited, usually keep H2 low so others can make acetate, ATP, etc, but without low H2 these reactions are therm unfavorable so use the acid producing pathway

Front 23

function of Fe protein in N2 fixation

Back 23

electron acceptor for FD, transfers to MoFe. uses ATP to lower redox potential of electrons for transfer.

Front 24

how do acetogens reoxidize NADH

Back 24

use CO2 as an electron sink

Front 25

major metabolic groups in cow rumen

Back 25

methanogens, cellulose-fermenting, syntrophic

Front 26

why do sulfate reducers use adenosine 5' phosphosulfate intermediate instead of doing it directly

Back 26

would require too much energy to lower redox potential of the electrons, so use ATP this way

Front 27

what enzyme would you think you need to get H2 from Glu that most anaerobes don't have

Back 27

bifurcating hydrogenase

or

pyruvate:ferredoxin oxidoreductase

want to form H2 and regenerate electron carriers, could increase ATP yield

Front 28

if a propionic doesn't have a functional PEP carboxytransphosphorylase, what would you need to add to the medium to allow growth?

Back 28

malate, succinate, or fumarate; can go to methylmalonylCoA and restart cycle back to oxaloacetate. without this enzyme it couldn't make PEP into oxaloacetate using CO2 fixation so it has to use the other pathway.

Front 29

pyruvate:ferredoxin oxidoreductase

word eq, cofactors, org/condition

Back 29

pyruvate + CoA + FDox -> acetylCoA + CO2 + FDred + 2 H+

thiamine pyrophosphate, CoA, FD

Clostridia, acetogens anaerobic metabolism to get pyruvate to acetylCoA without producing any NADH, use CO2 and make carbon in high PP of H2

Front 30

pyruvate:formate lyase

word eq, cofactors, org/condition

Back 30

pyruvate + CoA -> acetylCoA + formate

free radical carriers like glycine, tyrosine

in enterics, free radical cleavage, in mixed acid fermentation

Front 31

alpha-acetolactate synthase

word eq, cofactors, org/condition

Back 31

2 pyruvate -> CO2 + alpha-acetolactate

thiamine pyrophosphate

enterics using 2,3-butanediol fermentation

Front 32

molar growth yield to ATP production

Back 32

(X gram cells per mol Glucose (given))/(10.5g cell/ mol ATP) = X ATP/Glu

Front 33

how would you do an experiment to see if an org uses ED or EMP pathway

Back 33

label 1 carbon:

ED will give labeled CO2, EMP won't

label 3 carbon:

EMP will give labeled CO2, ED won't

Front 34

randomizing v. acrylate pathway for propionate metabolism

Back 34

acrylate: one product with one labeled carbon

randomizing (methylmalonylCoA): two products with two different labeled carbons, since intermediate is symmetric

Front 35

how do clostridia reoxidize FD?

Back 35

by using hydrogenase to make H2

Front 36

why would pyruvate:ferredoxin oxidoreductase be selected for in obligate anaerobes?

Back 36

makes hydrogen production favorable even at high PP

Front 37

phosphoenol pyruvate-carboxyltransphosphorylase equation

Back 37

diphosphate + oxaloacetate -> phosphoenolpyruvate + CO2

Front 38

function of P clusters in nitrogenase

Back 38

electron transfer (2) so nitrogen can go to ammonia

Front 39

function of H cluster in Fe-Fe hydrogenase

Back 39

active site, where catalysis of H2 production happens

Front 40

what can you conclude about an org that has Co dehydrogenase/acetyl-CoA synthase

Back 40

it is anaerobic and fixes CO2