BICH 411 exam #4 NITROGEN, SULFUR & AMINO ACIDS

nitrification?

The biological oxidation of ammonia into nitrites and nitrates.

nitrification reaction equation?

NH3 -> NO2- -> NO3-

nitrification occurs only in?

prokaryotes

first reaction of nitrification step 1 catalyzed by?

AMO ammonium monooxygenase

first step of nitrification equation step 1?

NH3 + O2 + 2e- -> NH2OH + H2O

first product of nitrification step 1?

hydroxylamine

NH2OH

second reaction of nitrification step 1 catalyzed by?

HAO hydroxylamine oxidoreductase

second reaction of nitrification step 1 product?

nitrite

NO2-

second reaction of nitrification step 1 equation?

NH2OH + H2O -> NO2- + 5H+ + 4e-

what powers the electron transport chain of nitrifying bacteria?

the electrons from ammonia

nitrification step two reaction catalyzed by?

NOR nitrite oxidoreductase

2nd step of nitrification reaction equation

NO2- + 1/2O2 -> NO3-

second reaction nitrification goes from nitrite to?

nitrate

NO3-

bacteria that can go from ammonia to nitrate directly?

comamox bacteria

denitrification

The biological reduction of nitrate to molecular nitrogen.

denitrification reaction equation

NO3 - → NO2 - → NO, N2O → N2

denitrification first step catalyzed by?

nitrate reductase

denitrification first step equation

NO3 - + 2H+ + 2e- → NO2 - + H2O

denitrification second step catalyzed by?

nitrite reductase

denitrification second step reaction equation?

NO2 - + 8H+ + 6e- → NH4 + + 2H2O

NH4 from denitrification can?

stay in the cell but needs an enormous amount of assimilating power

how to allow nitrite to be converted to assimilated ammonia?

photosynthetic mechanism which has a large reducing power

photosystem 1

A powerful reductant. Transfers electrons to ferredoxin

ANAMMOX:

ANaerobic AMMonium OXidation

generates dinitrogen

50% of all N2 in the oceans

ANAMMOX reaction equation

NH4 + + NO2 − → N2 + 2H2O

nitrogen fixation

The process of converting N2 into biologically available nitrogen

only bacteria can do this

nitrogen fixation reaction equation

N2 → NH3 (NH4 + )

nitrogen fixation equation

what does it take to do this?

N2 + 6H+ + 6e- → 2NH3

organisms cannot use dinitrogen only in chemical reactions because its very

innert, must be converted to NH3 to be assimilated

full required equation for nitrogen fixation

N2 + 10H+ + 8e- + 16 ATP → 2NH4 + + H2 + 16ADP + 16Pi

Nitrogen fixation requirements

Nitrogenase

• Strong reductant (ferredoxin)

• ATP

Anaerobic conditions

nitrogen fixation cannot occur if?

in the presence of oxygen

the enzyme is inactivated in <1 min in the presence of oxygen

to get reducing power for nitrogen fixation?

can use NADPH or photosynthesis to make reduced ferrodoxin

the most biologically significant hydrogenase reaction occurs in

the roots in plants by a bacteria called rhizobium

rhizobium->

A symbiotic bacterium that lives in the nodules on roots of specific legumes and that incorporates nitrogen gas from the air into a form of nitrogen the plant requires

rhizobium gives nitrogen in the form of

ammonium

rhizobium makes a type of hemoglobin

what is it and why does it need it?

Leghemoglobin binds any O2 that makes its way into the nodules, makes completely anaerobic environment for the nitrogenase

sulfur assimilation reaction equation

SO4 2- ->SO3 2- ->H2S ->Cys, Met

SO4 2-

Sulfate

SO3 2-

Sulfite

H2S

sulfide

three paths of sulfur assimilation

Dissimilatory reduction

Assimilatory reduction

Dissimilatory oxidation

sulfate must be activated before it can be used?

use ATP

must adenylate the ATP

adenylation of ATP equation

SO4 2- + ATP → APS + PP

adenylation of ATP makes what

Adenosine-5'-phosphosulfate (APS)

assimilatory reduction catalyzers?

ATP sulfurylase, APS kinase, PAPS reductase, sulfite reductase

assimilatory reduction step 1

catalyzed by?

ATP sulfurylase

assimilatory reduction step 1

reaction equation?

SO4 2- + ATP → APS + PP

assimilatory reduction step 2

reaction equation?

APS + ATP → PAPS + ADP

assimilatory reduction step 2

catalyzed by?

APS kinase

assimilatory reduction step 3

reaction equation?

PAPS + NADPH + H+ → SO3 2- + PAP + NADP

assimilatory reduction step 3

catalyzed by?

PAPS reductase

PAP combines with H2O to make

AMP + Pi

assimilatory reduction step 4

catalyzed by?

sulfite reductase

assimilatory reduction step 4

reaction equation?

SO3 2- + electron donor → H2S + oxidized donor + 3 H2O

electron donor from assimilatory reduction reaction?

NADPH Ferredoxins Flavins

what is the purpose of dissimilatory oxidation?

reverses rxn

H2S-> S -> SO3 2- -> SO4 2-

uses electrons from H2S to regenerate sulfate SO4 2-

protein amino acids account for

half of the cells mass

how do cells make amino acids

glycolysis

Pyruvate → Ala, Val, Ile, Leu

Glycerate-3-P → Ser, Gly, (Cys)

aromatic amino acids use both glycolysis and PPP to make the amino acids:

PEP and erythrose-4-p-> Phe, Tyr, Trp

how do cells make amino acids

PPP

Ribose-5-P → His

how do cells make amino acids

TCA cycle

2-Ketoglutarate → Glu, Gln, Pro, Lys, Arg

Oxaloacetate → Asp, Asn, Thr, Ile, Met (Cys)

essential amino acids

Val, ile, leu, phe, Trp, His, Lys, Arg, Thr, Met

CO2 tracer experiments establishing the path to AA includes

CO2 + pyruvate

(carboxylate)

CO2 + pyruvate =

makes what

carboxylation

pyruvate carboxylase

makes oxaloacetate

oxaloacetate goes to where?

the TCA cycle

oxaloacetate + acetate (2 extra Cs) =

Asp, Met, Thr and Ile

Asp, Met, Thr and Ile have?

the same specific activities

oxaloacetate (loses a C) + acetate/ acetyl co a=

2-ketoglutarate -> Glu, Pro

2-ketoglutarate + 14CO2=

Arg

carboxylation

2-ketoglutarate if you lose carbon =

Lys

decarboxylation

key reactors for amino group transfer

alpha-ketoglutarate, glutamate and glutamine

TRANSAMINATION using glutamate equation

glutamate + 2-ketoacid → 2-ketoglutarate + amino acid

2-ketoglutarate from transamination reaction can be used in?

the TCA cycle for Carbon utilization

AMINATION using glutamine equation

glutamine + acceptor → amino-acceptor + glutamate

the amino-acceptor from amination can be used?

Nitrogen utilization

alpha ketoglutarate-> glutamate catalyzed by?

glutamate dehydrogenase GDH

glutamate-> glutamine catalyzed by?

glutamine synthetase GS

alpha- ketoglutarate -> glutamate products and reactants

NADPH2 + NH3-> NADP+

glutamate-> glutamine products and reactants

ATP + NH3 -> ADP + Pi

The GDH/GS path

2 NH3 + α-ketoglutarate + NADPH + ATP → glutamine + ADP + Pi

The GDH/GS path ATP / NH3 ratio

[ATP]/[NH3 ] = 0.5

glutamine-> glutamate

reverse reaction of glutamine synthetase

glutamate synthase (GLT/GOGAT)

The GS/GOGAT path

2 NH3 + α-ketoglutarate + NADPH + 2ATP → glutamine + 2ADP + 2Pi

The GS/GOGAT path ATP/NH3 ratio

[ATP]/[NH3 ] = 1

The GS/GOGAT path products and reactants

NAD+ + alpha-KG-> NADH

glutamate-> alpha-ketoglutarate

reversed reaction catalyzed by?

glutamate dehydrogenase GLUD

glutamine synthetase must be

adenylylated which will inactivate it

inactive glutamine synthetase=

GS-AMP

enzyme that catalyzes the adenylylation of GS?

ATase

ATase must be ?

urydylated to promote activation of glutamine synthetase

regulator of the uridylation mechanism =

UTase

H2O-> UMP (hydrolase : high N)

UTP-> PPi (transferase: low N)

glutamate to proline requires

(phosphoryl.) ATP-> ADP

NADPH + H-> NADP+ + Pi

NADPH + H+-> NADP+

glutamate to arginine requires

acetylCoA-> CoA (acetylation of amino)

amino group blocked by acetylation then process similar to proline

protecting the amino group when converting glutamate -> arginine does what?

protects from cyclization

between making glutamate into arginine you create?

ornithine needs one extra carbon and 2 nitrogens to bcm Arg

ornithine to arginine how?

the urea cycle

enzyme that makes carbamoyl phosphate in the mitochondria using ammonia

carbamoyl phosphate synthetase 1

where is ammonia coming from in the carbamoyl phosphate rxn

some from glutamate dehydrogenase GLUD

carbamoyl phosphate synthetase 1 rxn

in mitochondria

2ATP + HCO3 - + NH3 → 2ADP + Carbamoyl phosphate + Pi