Biochem 2 Exam 1 Review

What are fates of excited electrons?

There are 4 fates: (Note: Quantum = equivalent level of energy) o Heat Loss: The energy can be dissipated as heat through redistribution into atomic vibrations within the pigment molecule o Fluorescent Light: Occurs only for saturating light. A photon of fluorescence is emitted as the electron returns to a lower orbital. The photon has a longer wavelength, and hence, a lower energy than the quantum of excitation. o Resonance Energy Transfer: The energy can be transferred by resonance to a neighboring molecule if the energy level between the two corresponds to the quantum of excitation energy. o Energy Transduction: In raising an electron to a higher energy orbital, the energy of excitation makes the pigment molecule a potent electron donor. This is the transduction of light energy into chemical energy. § This is the essence of Photosynthesis

What are the intracellular nitrogen donors, and their relative quantitative importance.

There are two donors: Glutamate and Glutamine Hight Ammonia: - Glutamate = 75% of N2 donated - Glutamine = 25% of N2 donated - GDH pathway assimilates 75% and GS assimilates 25% Low Ammonia: - GS assimilates 100% of ammonia and converts 75% ofglutamine to glutamate

Understand the absorption spectra

o Additional pigments (accessory light harvesting pigments), serve to absorb light wavelengths that outside of the range of absorption of the chlorophyll pigments such as Carotenoids and phycocyanobilin o The absorption spectra show the maximum absorptions at around 425/450 nm for blue and 625/650 nm for red. Less absorption at around green, this results in the color green being shown. o Plants with both chlorophyll a+b can harvest a wider spectrum of incident energy. Chlorophyll absorbs blue and red light. The ground state S0. with blue photon, the state is S2 and with red photon the state is S1. · S2 is converted to S1, since S1 is the most stable state.

What are the light reactions?

*Illuminated chloroplasts, in the absence of CO2, generates oxygen (waste), NADPH and ATP. *Takes place in the interior of thylakoid vesicles (lumen).

What are the dark reactions?

*Reaction takes place once the illuminated chloroplast is placed, or even in the dark, in the presence of CO2 fixation. *NADPH and ATP from light reaction used to drive the process of hexose (sugar) formation from CO2 fixation. * Dark reactions take place in the stroma.

what factors control/affect the nitrogen and nitrogenase activity?

- ADP inhibits acitivty - NH+ inactivates transcriptional activator - Some organisms have a 3rd controlling mechanism, ADP-ribosylation of the nitrogenase reductase subunit.

How is glutamine synthetase controlled?

- Controlled allosterically, by covalent modification and through gene expression. - Feedback Inhibition/Allosteric Regulation: Amp competes with ATP for binding at the ATP substrate site. Gly, Ala, and Ser compete with Glu for binding at the active site. Carbamoyl-P binds at a site that overlaps with both the Glu site and the site occupied by y-PO4 of ATP. Gly and Ser will accumulate if the cell has enough purines which require glutamine for their synthesis, thus they are indicators of glutamine abundance. - Covalent Modification: Each glutamine synthase subunit can be adenylated at the tyrosine residue, this inactivates glutamine synthase.

Caroteniods

- have a double conjugated system, and it allows pigment through the spectrum. The 2 primary roles are: 1. Light harvesting 2. Photoprotection through destruction of reactive oxygen species. a. Leaf colors during autumn are due to persistence of some of these pigments. Carotenoids absorb blue and appear yellow red.

Transaminations: nitrogen donor, cofactor, reversibility

- involve transfer of an alpha-amino group from a donor (usually Glutamate) to the alpha-keto position of an alpha-keto acid - Reactions are usually readily reversible. - The excess or lack of Glutamate determines the direction of the reaction. Excess = forward (usually the direction it goes in). - AN ESSENTIAL COFACTOR of aminotransferases is pyridoxal phosphate. The intermediate pyridoxamine is an amino donor.

Know the reaction mechanism of glutamine synthetase since it is found for many enzymes.

-Catalyzes the ATP-dependent amidation of the y-carboxyl group of glutamate to form glutamine -Reaction proceeds via a y-glutamyl-phosphate intermediate, and GS activity depends on the presence of divalent cations such as Mg+ -The amide-N of glutamine provides the nitrogen atom in these biosyntheses

Amino acid classifications: families, and members of each family

1.) ɑ-ketoglutarate Glutamate Glutamine Proline Arginine Lysine* (bacteria) Pneumonic: "G.G, P.A.L" 2.) Oxaloacetate Aspartate Asparagine Methionine Threonine Isoleucine Lysine* Pneumonic: TAMALI (the food spelled wrong) 3.) Pyruvate Alanine Valine Leucine Pneumonic: P(yruvate)V.A.Leu ("p value") 4.) 3-PG Serine Glycine Cysteine 5.) PRPP & ATP Histidine 6.).Phosphoenolpyruvate & Erthrose-4-P (aromatics) Phenylalanine Tyrosine tryptophan

The steps of nitrate assimilation: how many electrons involved and what metals are involved? How many reactions in converting nitrate to ammonia? What are the source of electrons?

2 steps: 1.) 2 electron reduction of nitrate to nitrite. Catalyzed by nitrate reductase. 2.) 6 electron reduction of nitrite to ammonia. Catalyzed by nitrite reductase. MoCO (molybdenum cofactor) necessary for both nitrate reductase activity and assembly of nitrate reductase subunits into active form. Photosynthetically reduced ferredoxin

What is happening in the lumen and stroma?

A proton gradient is built as the proton moves down the gradient as the synthesis is occurring.

Pyruvate family: alanine synthesis, precursors for branched chain amino acids, role of thiamine pyrophosphate and of shared enzymes, leucine synthesis pathway mimicks what pathway.

Alanine synthesis: Alanine is synthesized by a glutamate-alanine transaminase in all organisms. Precursors: Pyruvate / Threonine Thiamine pyrophosphate initiates both synthesis pathways by combining with pyruvate to form thiamine. It is a common enzyme between Isoleucine and Valine. The other shared enzymes assist in transamination processes as well. Leucine synthesis pathway mimics a reaction in the TCA cycle. (The TCA cycle is derived from the leucine synthesis pathway).

What is the difference between cyclic and noncyclic photophosphorylation?

Cyclic Phosphorylation: a way to recycle electrons that can be used for ATP synthesis. It has an additional protein called cytochrome b6. Makes ATP but not NADPH or O2. Noncyclic Phosphorylation: O2 evolved and NADP+ is reduced Difference between the two: in cyclic phosphorylation the electrons comes from P700 of PSI and the electrons are NEVER donated to NADP+. The electrons involve plastoquinone and that protein is pumped into the lumen and O2 is NOT evolved. This process is 20 times slower than noncyclic photophosphorylation. This may overcome the ATP deficit produced by the Z-scheme.

Essential and nonessential amino acids (what does this mean), difference between plants, bacteria and higher animals. Do not memorize the amino acids for this classification.

Essential amino acids are those which cannot be synthesized by humans and must be acquired from the diet. Most Bacteria and plants can synthesize these via long and complex pathways (using Ammonia). Non-essential AAs = ones we can synthesize (10AA for humans)

Ferredoxin shows up a lot. Why?

Ferredoxin: small proteins containing iron-sulfur clusters. They act as an electron acceptor associated with PSI. Key takeaway = important for electron transfer.

Amino acid degradation: what is difference between glycogenic and ketogenic amino acids, how nitrogen is removed, and where does it go, alkaptonuria and how are symptoms prevented.

Glycogenic amino acids: can be converted to glucose Ketogenic amino acids: can be used to make fatty acids/ ketone bodies Nitrogen removal: early step in degradation of carbon skeletons of amino acids. (1) Loss of nitrogen by transamination to alpha-ketoglutarate (forms Glutamate!) OPTION A) The glutamate nitrogen is donated to OAA, which forms Aspartate. Aspartate forms fumarate, which is reconverted to OAA. OPTION B ) The nitrogen of Glutamate is lost due to Glutamate Dehydrogenase (forms alpha-ketoglutarate and AMMONIA) - uses NAD as a cofactor Ammonia enters the urea cycle → excreted as urea, ammonia, or uric acid

The logic of herbicides (what type of pathways targeted), but knowledge of specific herbicides is not required.

Herbicides kill weeds. Plants can make all 20 amino acids, so these compounds target precursors of the essential amino acids (not the ones we produce, so our precursors are not affected) so that they are not toxic to us, but will cause the plant to die.

Limitations of Rubisco

If O2 is used instead of CO2 by rubisco, then the products are 3PG and glycolate. This reaction occurs at about 25% of rate of CO2 fixation. Glycolate can be converted to glyoxylate, and then to glycine and serine. The conversion to serine releases CO2. This is called photorespiration since CO2 is released

How do plants avoid the problem of the reaction of Rubisco with oxygen?

If reacted with O2, not CO2 , then RuBP (essential CO2 acceptor) is lost and plant diminished. The product would be 3-phopshoglycerate and phosphoglycolate. Oxidation and dephospho rylation convert glycolate to glyoxylate. In he mitochondria 2 glycines confer into one serine and one CO2. By converting 2 glycine to serine it creates hydroxypyruvate, which can be reduced to glycerate. Glycerate can be phosphorylated to 3PG and can fuel resynthesis of RuBP by the Calvin cycle.

How were chloroplasts used to demonstrate the chemiosmotic mechanism of ATP synthesis?

In Photophosphorylation (light driven ATP synthesis), PMF can create ATP by a chemiosmotic mechanism. In mitochondria the pH gradient is a unit of 1 while in chloroplast it is a unit of 3. PMF's charge component contributes more in chloroplast than the concentration gradient. An artificial pH gradient was shown to be sufficient for ATP synthesis in chloroplast.

What is the difference between the lamella and Granum?

Lamella connects and separates the thylakoid stacks, which are the grana. Granum are the flattened discs that are stacked on top, which increase the surface area and volume ration and the small internal volumes quickly accumulate ions.

Chloroplasts structure and function are very important.

Lamellae - Paired folds that extend throughout the organelle, connecting thylakoid vesicles. (location of PSI) Thylakoid Vesicles - flattened sacs or discs which occur in stacks called grana. Granum - A single stack of thylakoid vesicles. Different grana are interconnected through lamellae. (location of PSII) Stroma - The membrane-bound aqueous portion of the chloroplast, soluble, which the lamellae run through. Intermembrane space - A fluid filled portion between the inner and outer double membrane. Thylakoid Lumen - Aqueous membrane-bound interior of the thylakoid vesicles. Serves an important function in the transduction of light energy into ATP formation. (During light reactions, Protons enter the Lumen and creates PMF)

Nitrification

Oxidation of ammonia, converting it to nitrite and nitrate. Makes nitrogen readily available for plants as nitrate is more soluble than ammonia for absorption. Process done by bacteria

Where does photosynthesis occur in plants and bacteria?

Photosynthesis occurs in the membranes. Bacteria: membranes are a major component to the cytoplasm Plants: membranes are in large organelles (plastids) called Chloroplast In plants, photosynthesis occurs in the chloroplasts, but more specifically, it occurs within the Thylakoid membrane. In bacteria (Cyanobacteria), photosynthesis occurs in their outer double membrane, with the photosynthetic membranes filling up the cell interior.

What is a reactive center?

Photosynthetic unit: o Consists of many chlorophyll molecules but only a single reaction center. The job of most of the chlorophyll is to harvest light energy and funnel it, via resonance energy transfer, to the reaction center. Reaction Center: o The Reaction center is a special pair of photochemically reactive chlorophyll A molecules. It is here where the photosynthesis occurs.

What are the two photosystems and what are their functions?

Photosystem I (electron donor/reducing agent): Has a maximal absorption at 700nm, does not evolve O2, and uses ferredoxins as terminal electron acceptors. PSI provides reducing power in the form of NADPH. Reaction Center = P700 Photosystem II (electron acceptor/oxidizing agent): Has a maximal absorption at 680nm, uses quinones as terminal electron acceptors, and splits water molecules to evolve O2 which also gives electrons. Reaction center = P680. Transfers electrons to PSI. Eukaryotes have both photosystems, while photosynthetic bacteria (excluding cyanobacteria) only have PSII, but they DO NOT generate O2.

What is the electron source for NADPH and ATP synthesis in plants and bacteria?

Plants: water is the electron source. Bacteria: water, H2S, isopropanol, or other oxidizable (reduced) compounds are the electron source.

Histidine synthesis: precursors, role of ATP

Precursors: PRPP and ATP as carbon precursors. ATP is partially altered and will help to release an intermediate in purine synthesis.

Similarities in the pathways of arginine and proline synthesis, cyclization and its prevention, mechanism of activation, biological reductant.

Proline synthesis (start with Glutamate) 1.) Phosphorylation activation by ATP 2.)Reduction 3.)Cyclization 4.)Reduction Arginine synthesis (start with Glutamate): 1.) Block with AcetylCoA 2.) Phosphorylation 3.) Reduction 4.) Transamination with Glutamate as nitrogen donor 5.) Unblocking (remove acetate group) (MAKES ORTHININE) 6.) Carbamoylation (the compound has entered the mitochondria) 7.) Activation by ATP 8.) Substitution by Aspartate 9.) Breaking of C-N bond, half of the molecule continues as ARGININE (N-side is left behind) (shared highlighter colors = shared steps/ similarities) Both reactions follow a similar pattern in that they contribute to ornithine synthesis.

Where are protons pumped in the process? What steps, and into what compartments?

Protons are pumped into the lumen

What are the reactions of Rubisco? How is Rubisco activity controlled?

Rubisco forms: - E form: inactive form - EC form: carbamylated form (still inactive) - ECM form: active form Rubisco is found in the chloroplast stroma and it catalyses reactions of CO2 or O2. It binds CO2 and RuBP to Mg2+. Rubisco is mediated by rubisco activase (a regulatory protein). Rubisco activase binds to E form of rubisco near its catalytic site which promotes the release of RuBP. Rubisco then becomes activated by carbamylation and Mg2+ binding. Rubisco activase is activated by light, thus LIGHT IS THE ULTIMATE ACTIVATOR OF RUBISCO. Rubisco is inhibited when RuBP binds to the E form of rubisco.

Function of Carboxysome (bacterial solution to rubisco's problems):

Rubisco problems are low affinity for CO2, low catalytic rate, O2 as substrate Carboxysomes concentrate CO2 100-1000X Cytoplasmic CO2 converted to HCO3- Carboxysome has carbonic anhydrase (HCO3- to CO2) and the CO2 saturates Rubisco Carboxysome prevents CO2 efflux and O2 influx

Nitrogen fixation and nitrogenase. What organisms do this? What are its requirements (reductant, energy, etc)? What are its components (the two protein components), and what do they do?

Bacteria are the only organisms that do this. All nitrogen fixation requires is the enzyme nitrogenase, a strong reductant (such as ferredoxin), ATP, and O2-free conditions. The enzyme contains TWO components: the Fe-protein (nitrogenase reductase) and the MoFe-protein (nitrogenase). The Nitrogenase reductase hydrolyzes two ATP per electron transferred or 16 per N2. ATP is used to overcome the activation energy required to break the double bonds on N2. This component is very O2 sensitive. The Nitrogenase is a alpha2beta2 protein. Each alpha/beta dimer contains a p-cluster and the FeMo-Cofactor. This component is also very O2 sensitive. This reaction involves electron transfer that starts with reduced ferredoxin (has a greater reduction potential than NADPH). The reductase is the electron donor. ATP hydrolysis is coupled to electron transfer from the reductase to the nitrogenase component. This is a SLOW process.

Carbamoyl-P synthetase, precursor for which compounds, most unusual aspect of reaction. How many enzymes in higher animals, and where are they located.

Carbamoyl-P is unusual because it consumes 2 ATPs. CPS-I is an enzyme located in the mitochondria of higher organisms (where the ATP is). Uses ammonia as a nitrogen source. Carbamoyl-P is a precursor for citrulline, arginine, and urea + 2 free nitrogens (a few other intermediates as well).

What is chlorophyll? What is its function? What does it contain (in terms of metals, and functional groups)?

Chlorophyll: o Magnesium-containing substituted tetrapyrroles. o Good absorber of light because of aromaticity (resonance). o Transduce light energy into the chemical energy of a redox reaction. 2 types: o Chlorophyll A, and Chlorophyll B. Their absorption differs. o They differ in their R groups on pyrrole II § A has a CH3 R group § B has a CHO

How does light control CO2 fixation? Thioredoxin and ferrodoxin involvement is this control.

Co2 fixation requires ATP and NADPH or else it is at a halt and Calvin cycle cannot continue. 1.) Light create pH changes in the chloroplast compartments (stroma and thylakoid lumen) and as the stroma pH rises, CO2 fixation is activated. 2.) A reducing power is created by the light energy. Illuminated chloroplast starts the electron transport, which produced a reducing power in the form of reduced ferredoxin by ferredoxin-thioredoxin reductase. 3.) Thioredoxin is produced by a pair of sulfahydryls that are oxidized two form disulfide bridge. 4.) Light creates a movement of MG2+ ions to thylakoid vesicles to stroma. 5.) Mg2+ activates ribulose bisphosphate carboxylase and fructose-1,6-bisphosphate enzymes. 6.) Meaning the flow of Mg2+ into the stroma is due to the light driven proton pumping which stimulates CO2 fixation.

Methionine synthesis, how sulfur is added, vitamins and cofactors involved, mechanisms that result in accumulation of homocysteine, methyl group addition, transsulfuration pathway.

Cofactors: Succinyl CoA (activating group) , Cysteine added (source of the sulfur!), pyruvate and an extra nitrogen are removed, leaving a SH group. Then a methyl group is supplied by the cofactor THF , forming Methionine. SAM (S-adenosylmethionine) is derived from methionine and reacts with methyl transferases (it is a methyl donor) which will generate homocysteine. Homocysteine accumulation results from low folate, low B6 or low B12. (HEART DISEASE RISK- form plaques)

Aromatic family: precursors, endproduct of common pathway, regulation of first reaction, (can ignore tryptophan synthesis, except know which compounds are required for it synthesis), conversion of phenylalanine and tyrosine, and disease that results from problems with the interconversion.

Common precursor: Chorismate Chorismate Synthesis starts with Erythrose-4-P combining with PEP. (called Shikimate Pathway) Tyrosine Synthesis: (100% REQUIRED molecule) (1) Rearrangement of chorismate (add NAD+) (2) Transamination by addition of Glutamate (3) Will have NH3 group AND OH group in finished compound Phenylalanine Synthesis: (can be converted to Tyrosine) (1) Rearrangement of Chorismate (add Without the enzyme monooxygenase to make the Phe→ Tyr conversion, Phenylalanine will accumulate and cause phenylketonuria (neurological degradation)

Nitrogen Fixation

Conversion of N2 to ammonia (NH4+) occurs only in bacteria ANAEROBIC Animals can do neither of these processes so they must acquire nitrogenous compounds from either plants or bacteria. Animals release nitrogen as ammonia, urea, and possibly uric acid. Occurs during animal release of waste or decomposition.

Denitrification

Conversion of nitrate to N2, which is released back into the environment. Done by denitrifying bacteria and meant to provide bacteria with electron acceptor other than O2 for energy generation. AEROBIC process and since O2 is preferred electron acceptor, any oxygen present will interfere with this process form the beginning.

Nitrate assimilation

Conversion of nitrate to ammonia (NH4+). occurs in some plants, fungi, and bacteria AEROBIC process Animals can do neither of these processes so they must acquire nitrogenous compounds from either plants or bacteria. Animals release nitrogen as ammonia, urea, and possibly uric acid. Occurs during animal release of waste or decomposition.

Principles of feedback inhibition, the covalent modification, and gene expression controls: what metabolites are involved? (I will not ask specific inhibitors, but what properties are shared by the inhibitors.)

Covalent modification and Gene expression are both controlled by Utase/ UR and

What is the effect of high and low glutamine on these controls?

Covalent modification: o High: UR is active, which results in PIIA formation (instead of PII-UMP). PIIA interacts with ATase and adenylates GS. This form of PII is called PIIA o Low: UTase is active, and PII-UMP is formed, its interaction with ATase results in deadenylylation of GS. This form of PII is called PIID · Gene expression: o High (nitrogen excess): this results in PIIA which interferes with phosphate transfer from NRII to NRI. NRI-P ks a transcriptional activator, if unphosphorylated, it becomes inactive and the gene for GS is not expressed. o Low (nitrogen limitation): Results in PIID formation and phosphate transfer from NRII to NRI. NRI-P, a transcriptional activator, turns on the gene for GS.

3-phosphoglycerate family: serine, glycine, and cysteine synthesis; synthesis of C1 intermediates, sulfur assimilation (what compound is environmental sulfur source, what is actually incorporated into amino acids). What is the major donor for sulfur in various biosyntheses.

Serine: (requires Zn and B6) - REVERSIBLE (1) Start with 3PG (glycolytic intermediate- produced in C fixation) (2) Oxidation (3) Transamination (4) Dephosphorylation Glycine: (derived from serine) -SOURCE OF THF, can be disassembled (1) Start with serine (2) Add THF (takes a methyl group away) Cysteine: (derived from serine- common bacterial pathway, sulfide addition)- MAJOR SULFUR DONOR (1) Start with serine (2) Add Acetyl-SCoA (3) Add H2S (will remove Acetyl-SCoA) (4) SH will remain in the product Sulfide Synthesis (required for cysteine synthesis) Reduction from sulfate to sulfide. Consumes many ATP - Activation and reduction steps involving 3 NADPH. Know that thioredoxin is involved and forms disulfide bond.

What are the similarities between electron transport in oxidative phosphorylation and photosynthesis? What components are in common? What components are not in common? How is the proton gradient generated?

Similarities: Both occur in living cells Both use a multi-step electron transport chain at membranes, allowing the establishment of a proton gradient due to proton pumping that can be used for ATP synthesis. Common Components: Quinones Cytochromes (Fe-S clusters)

What are the products of photosynthesis and how are they made? What is the source of electrons?

Summary: They are produced via the electron transport chain ( & z-scheme) driving ATP synthase by sequestering the electrons energy in tiny steps to generate a proton gradient. -Electrons in the light absorbing pigment chlorophyll are excited by light and will pass between other chlorophyll molecules (resonance energy transfer) until it reaches a reaction center which is capable of photosynthesis. -The electron will be used to generate a proton gradient as it loses energy (which is conserved in tiny steps) in photosystem II via a VERY strong oxidant and many intermediate steps. The proton gradient will be used to activate ATP synthase and form ATP (and then glucose). Photosystem II will then effectively replace the electron which chlorophyll has lost by extracting it from water using its strong oxidant: H2O → ½ O2 + e- -The electron will be energized as it passes through photosystem I , generating reducing power (strongest in nature) and facilitating the reaction: NADP+ → NADPH *Electron source is (H2O): - loss e- from chlorophyll -energize (exicte) for NADPH synthesis -Chlorophyll extract a e- from H2O

Carbon dioxide fixation. Which reactions incorporate CO2? What are the unique reactions of the Calvin-Benson cycle? Where are ATP and NADPH used?

The Calvin cycle is near or in the stroma. CO2 fixation: the net synthesis of carbohydrate from CO2 Reactions that incorporate CO2: yung Calvin Cycle Calvin cycle: 6CO2 + 6RuBP = 12 (3-phosphoglycerate) 12 (3-phosphoglycerate) = 1 (hexose) + 6RuBP Net Reaction: 6CO2 = 1 (hexose) (Riboluse-1,5-bisphosphate) = RuBP

Urea cycle: which steps in mitochondria, its function, how nitrogen enters the cycle, what tissue has enzymes of the cycle.

The Urea cycle is a mechanism to remove excess nitrogen- usually the nitrogen is ammonia generated from GDH via the deamination of glutamate. The ammonia and bicarbonate form a complex with Carbamoyl-P. It is a very energy intensive process and takes place in the tissues of the liver.

Final steps in arginine synthesis: common reactions with urea cycle.

The difference between the two: At the end of the urea cycle, arginase will convert arginine to Ornithine and Urea. Arginine synthesis will just stop at Arginine. Common final steps: aspartate substitution, and the final cleavage of the compound (most small steps are the same as well)

Asparate family: similarities with glutamate (α-ketoglutarate family), asparagine synthesis (mechanism of activation), control of first reaction of common pathway

The members are aspartate, asparagine, lysine (in bacteria), methionine, threonine, and isoleucine. Like glutamate family amino acids, almost all the chemistry is at the terminal carboxyl group, and this requires activation of the carboxyl group by similar mechanisms. Asparagine is synthesized in a reaction similar to the GS reaction (Fig 25.26). The carboxyl group is activated with ATP forming aspartyladenylate. All organisms have glutamine as the nitrogen donor. Bacteria can have a second enzyme that can directly use ammonia. In this case, for example E. coli, the organism has two enzymes. Leukemic cells require asparagine, and this can be used to attack them (see p 863).

What pathways assimilate ammonia and what are the products? What are the differences between the two pathways? What is the reductant?

The pathways that assimilate ammonia are glutamate dehydrogenase (GDH) and glutamine synthetase (GS). GDH pathway: catalyzes the reductive amination of alpha-ketoglutarate, with NADPH as the reducing agent. NADPH is in excess over NADP, so the reaction goes in the synthetic direction. GDH can assimilate ammonia into glutamate when high amounts of ammonia are present. GS pathway: catalyses the amidation of glutamate. This reaction requires ATP which is used to phosphorylate the carboxyl group. When ammonia is low, this pathway can first synthesize glutamine, then glutamate synthase uses glutamine as a nitrogen donor for the formation of glutamate. The difference in this pathway vs the GDH pathway is the amount of energy this pathway uses. The GDH pathway does not need to consume ATP to synthesize glutamate, whereas this pathway does. Reductant = Ferrredoxin

What is the Z scheme?

The sequence involves e-transfer from water via the water splitting component, to activated P680, to quinones (plastoquinones), to an Fe-S center in cytochrome, to plastocyanin, to P700, to membrane-bound ferredoxins, to soluble ferredoxins, to a reductase, to NADPH. Note the similarity to e-transport in oxidative phosphorylation.