Flashcards in Chapter 9: The Citric Acid Cycle Deck (62):
organisms that grow only in the absence of oxygen...avoid the gas by living in highly reduced environments like soil.....they use fermentation for energy!
depends on fermentation for energy needs, but they possess detoxifying enzymes and antioxidant molecules that protect against oxygen's toxic products.
not only possess the mech needed for detoxifying oxygen metabolites they can also generate energy using oxygen as an e- acceptor when the gas is present
-highly dependent on oxygen for energy production
- protection from its dangerous effects with mechanisms composed of enzymes and antioxidants
Facultative anaerobes and obligate aerobes use what methods of energy production?
- use oxygen to generate energy use the following processes:
citric acid cycle, electron transport chain and oxidative phosphorylation! (eukaryotes this is in the mitochondria! )
NADH and FADH2 act as what?
What is the electron transport chain? (ETC)
electrons are transferred from reduced coenzymes to an acceptor usually O2.
energy released by electron transport is captured in the form of a proton gradient that drives the synthesis of ATP
tendency for a specific substance to gain electrons
Standard reduction potential is measured how?
- in a galvanic cell relative to a standard hydrogen electrode. A standard cell has all solutes at [1.0M], gases= 1 atm, temperature = 25 C
What is the reduction potential for the half reaction (2H+) + (2e-) -----> H2 (g) against the standard hydrogen electrode?
(2H+) + (2e-) -----> H2 (g)
- Under these conditions the reduction potential of the hydrogen electrode is?
L> when measured agains the standard hydrogen electrode...H concentration is 1M.
Substances with reduction potentials lower than -0.42V are said to have?
lower affinity for electrons than does H+ (those with more negative values)
Substances with reduction potentials higher than -0.42V are said to have?
- a greater affinity for electrons than does H+(more positive values)
** ph for test electrode= 7......for each half reaction, ph of the reference electrode = 0 or the H+ concentration is 1.0M
A substance with a ___ reduction potential will receive electrons from a substance with a ____ reduction potential and the overall cell potential ( delta E knot prime) will be ___.
- more negative ( less positive)
- more positive
What is the formula for the relationship between delta E knot prime and delta G knot prime?
Delta G knot prime= -nFdelta_E_knot_prime
L> Delta G knot prime= the standard free energy
L> n= number of electrons transferred
L> F= faraday constant..... 96,485J/Vxmol
L> delta_E_knot_prime = difference in reduction potential between the electron donor and the electron acceptor under standard conditions!
What are the two coenzyme forms of nicotinic acid?
1. nicotinamide adenine dinucleotide (NAD)
2. nicotinamide adenine dinucleotide phosphate (NADP)
L> oxidized forms: NADH and NADPH
L> carry electrons for several enzymes in a group known as the dehydrogenates.
L> The enzymes that require NADPH usually catalyze biosynthetic reactions.
In most reactions catalyzed by dehydrogenates, the NAD+ (or NADP+) is bound only _____to the enzyme.
Riboflavin (Vitamine B2) is a component of two coenzymes what are they?
1. Flavin mononucleotide (FMN)
2. Flavin adenine dinucleotide (FAD)
FMN and FAD function as tightly bound prosthetic groups in a class of enzymes known as what?
Flavoproteins function as?
dehydrogenases, oxidases and hydroxylases. These enzymes catalyze oxidation-reduction reactions, use the isoalloxazine group of FAD or FMN as a donor or acceptor of two hydrogen atoms.
FMN plays a key role in the link between what?
- two-electron transferase rxns in the mitochondrial matrix and the one-electron transfer rxns of the electron transport chain as it can transfer one hydrogen atom at a time.
L> succinate dehydrogenase = flavoprotein
whats the equation for the overall potential of a half reaction?
electron acceptor - electron donor
What captures most of the aerobic cell's free energy ?
mitochondrial electron transport chain...
During the ETC electrons are transferred from ??
a redox pair with a more negative reduction potential (NADH/NAD+) to those with more positive reduction potentials
The last component in the ETC is what?
H2O/ 1/2 O2 pair:
1/2 O2 + NADH + (H+)-----> H2O + NAD+
A significant portion of the free energy generated as electrons move from NADH to O2 in the ETC is used to drive what?
In should be noted that in several metabolic processes, electrons move from redox pairs with more ___ reduction potentials to those with more ___ reduction potentials.
In the citric acid cycle, the acetyl groups carbon atoms are oxidized to __ and the electrons are transferred as __ to NAD+ and FAD+
- hydride ions
What is the overall net reaction for the citric acid cycle?
Acetyl-CoA + (3NAD+) + FAD + GDP + Pi----> 2CO2 + 3NADH + FADH2 + CoASH+ GTP + 2H+
What is the net equation for the oxidative decarboxylation with pyruvate?
Pyruvate + (NAD+) + CoASH ----> Acetyl-CoA + NADH + CO2 + H+
The pyruvate dehydrogenase complex?
a large multi-enzyme structure that contains three enzymes activities:
1. pyruvate dehydrogenase (E1) (pyruvate decarboxylase)
2. dihydrolipoyl transacetylase (E2)
3. dihydroxylipoyl dehydrogenase (E3)
Whats the first step in pyruvate dehydrogenase complex?
- pyruvate dehydrogenase catalyzes the decarboxylation of pyruvate...
L> nucleophile is formed when a basic residue of the enzyme extracts a proton from the thiazole ring of thiamine pyrophosphate (TPP which is the coenzyme form of thiamine...vitamin B1)
L> HETPP forms after the nucleophilic thiazole ring has attacked the carbonyl group of pyruvate with the resulting loss of CO2
Whats the next step in pyruvate dehydrogenase complex?
hydroxyethyl group of HETPP----> acetyl-CoA via dihydrolopoyl transacetylase
pyruvate dehydrogenase complex and Lipoic acid???
- an acyl transfer coenzyme that contains 2 thiol groups that can be reversibly oxidized, plays a crucial role in this transformation. It reacts with HETPP to form an acetylated lipoid acid and free TPP. The acetyl group is then trasnferred to the sulfhydryl group of coenzyme A.
pyruvate dehydrogenase complex:
- lipoid acid is reoxidized by what?
- dihydrolipoyl dehydrogenase.
L> FADH2 is deoxidized by NAD+...to form the FAD needed for oxidation of the next reduced lipoid acid residue. Mobile NADH can deliver e- to ETC and is replaced in the enzyme by another NAD+ molecule so that the cycle can repeat.
Pyruvate dehydrogenase is regulated by two mechanisms what are they?
-product inhibition and covalent modification
Pyruvate dehydrogenase regulation:
- The enzyme complex is allosterically activated by what three things?
- It is inhibited by what three things?
- NAD+, CoASH and AMP
- high concentrations of ATP and the reaction products acetyl-CoA and NADH.
L> these molecules also activate a kinase which converts the active pyruvate dehydrogenase complex to an inactive phosphorylated form.
( high concentrations of the substrates pyruvate, CoASH and NAD+ inhibit the activity of the kinase)
The citric acid cycle is composed of how many rxns and stages?
Briefly explain the two stages of TCA!
1. 2C acetyl group of acetyl-CoA enters the cycle by reacting with the four carbon compound oxaloacetate and two molecules of CO2 are subsequently liberated (rxns 1-4)
2. Oxaloacetate is regenerated so it can react with another acetyl-CoA (rxns 5-8)
Give a run through stage one of TCA!
1. acetyl-CoA -----> Citrate via citrate synthase
(H2O in and CoASH out)
2. citrate[cis-aconitate]isocitrate via aconitase
3. Isocitrate ----------isocitrate dehydrogenase-----> alpha-ketoglutarate
(NAD+ in and (H+) + NADH + CO2 out)
4. Alpha-ketoglutarate ----alpha-ketoglutarate-deyhdrogenase---> succinyl-CoA
( NAD+ in and NADH + H and CO2 out)
Give a run through stage two of TCA!
5. Succinyl-CoA ------succinyl-CoA synthetase----> Succinate
(GDP and Pi in.....GTP and CoASH out....) Now recycle !
6. Succinate----succinate dehydrogenase---> fumarate
( FAD in and FADH2 out)
7. Fumarate---fumarase----> Malate
8. Malate----malate dehydrogenase---> Oxaloacetate
( NADplus in and NADH + H out)
(cycle repeats after this for the second pyruvate)
- pathways that function in both anabolic and catabolic processes
L> catabolic: acetyl groups are oxidized to form CO2 and energy is conserved in reduced coenzymes
L> anabolic: several citric acid cycle intermediates are precursors in biosynthetic pathways
TCA intermediates that are precursors in other pathways???
- Ocaloacetate: gluconeogenesis substrate
- synthesis of aa's lysine, threonine, isoleucine and methionine
- alpha-ketoglutarate= aa synthesis for glutamate, glutamine, proline and arginine.
- Synthesis of prophyrins like heme...requires succinyl-CoA
- excess citrate molecules are transported in the cyto and cleaved to form oxaloacetate and acetyl-Coa. The latter is used to synthesize fatty acids and steroids like cholesterol.
reactions that replenish molecules required to sustain TCA's role in energy production since its anabolic processes drain the cycle
Ex of Anaplerotic rxns??
- rxn catalyzed by pyruvate carboxylase....high concentration of acetyl-CoA, indicator of insufficient oxaloacetate concentrations activates pyruvate carboxylase.
(increasing oxaloacetate production)
- synthesis of succinyl CoA
- It is achieved by what three enzymes?
1. citrate synthase
2. isocitrate dehydrogenase
- all are reversible
L> they operate far from equilibrium....high negative delta G values
- Citrate synthase, isocitrate dehydrogenase and alpha-ketoglutarate all catalyze reactions that represent what?
- important branch points.
L> strategies of control:
L> substrate availability
L> product inhibition
L> competitive feedback inhibition
- Explain why citrate synthase is a good regulation point?
L> succinyl CoA's role?
L> NADH and ATP?
- catalyzes acetyl-Coa + oxaloacetate ----> citrate
L> acetyl-CoA and oxaloacetate are low in concentration within the mitochondria in relation to the enzyme...any increase in substrate availability stimulates citrate synthase.
L>competitive inhibitor of citrate synthase...occupying acetyl-CoA's site when in excess and and citrate inhibits the enzyme by acting as an allosteric inhibitor
L> high NADH/NAD+ and ATP/ADP concentration = high energy in cell
L> therefore when the cell becomes metabolically active it causes a decrease in these ratios and an increase in citrate synthase activity
- explain why Isocitrate dehydrogenase is a good regulation point?
- activated by?
- inhibited by?
- stimulated by high concentration of ADP and NAD+...its inhibited by ATP and NADH.
- isocitrate dehydrogenase:
- explain the conversion of citrate to isocitrate and its importance?
- its reversible
- an equilibrium mixture of they two consisting of largely citrate....but the reaction is driven forward because isocitrate is converted to alpha-ketoglutarate quickly.
L> of the two only citrate can penetrate the inner mitochondrial membrane
L> when energy demands are met excess citrate leave the mitochondria....it is then cleaved making acetyl CoA and oxaloacetate. (acetyl CoA is used in other biosyntheses like fatty acids
L> acetyl CoA cannot cross the inner membrane ....citrate acts as a transport
L> oxaloacetate is used in other synthesis and conversion to malate.
L> Malate can re enter the mitochondria and be converted to oxaloacetate...or converted to pyruvate in the cytoplasm.
- citrate is an inhibitor of PFK-1...therefore it inhibits glycolysis
L> also an allosteric activator of fatty acid synthesis
- explain why alpha ketoglutarate is a good regulation point?
- when energy is low....this is activated...and alpha-ketoglutarate is retained in the cell.... as NADH rises the enzyme is inhibited and the alpha ketoglutarate becomes available for biosynthetic reactions. It is also inhibited by succinyl-CoA its product...and activated by AMP...an indicator of low energy.
What two enzymes outside the citric acid cycle regulate it?
- pyruvate dehydrogenase and pyruvate carboxylase which determine the rate pyruvate is used to generate energy
ex: if a cell is using alpha ketoglutarate for biosynthesis...oxaloacetate decreases and acetyl CoA increases ...since it increases it activates pyruvate carboxylase (inhibitor of pyruvate dehydrogenase) more oxaloacetate is formed...replenishing the cycle.
What is the glyoxylate cycle?
0 modified version of the citric acid cycle in plants, fungi, algae and protozoans and bacteria.
Where does the glyoxylate cycle occur?
in glyoxysomes ...occurs in the absence of photosynthesis?
How many reactions are in the glyoxylate cycle?
Explain which ones in the glyoxylate cycle are similar to the citric acid cycle?
- synthesis of citrate and isocitrate
L> HOWEVER.....the formation of citrate from oxaloacetate and acetyl-CoA and the isomerization of citrate to form isocitrate are catalyzed by glyoxylate specific isozymes
What two reactions are unique to the glyoxylate cycle?
Isocitrate -------> succinate and glyoxylate
- Sucinate ----> malate by mitochondrial enzymes .
- Glyoxylate + acetyl-CoA ----> malate
The glyoxylate cycle allows for the net synthesis of what?
larger molecules from two carbon molecules
The glyoxylate cycle allows for the net synthesis of larger molecules from two carbon molecules but why?
- decarboxylation reactions are bypassed (2 CO2 production) seen in TCA.
- by using two molecules of Acetyl-CoA...it produces one molecule each of succinate and ocaloacetate....succinate is used in glucose synthesis.
- oxaloacetate is used to sustain the cycle.