Unit Four Flashcards
1
Q
sa
What does Keq signify
A
The ratio of products over reactants present when a reaction is at equilibrium
2
Q
What does Q signify
A
The concentration of reactants at the present moment.
3
Q
What is the correlation of Gibbs free energy, Keq, and Q
A
When Keq is > 1, ∆G is Negative (favorable)
When Keq is < 1, ∆G is Positive (unfavorable)
When Keq =1, the concentration of reactants and products at equilibrium are the same
When Keq > Q it means the current reaction will go to the right
When Keq is < Q it means the current reaction will go to the left
4
Q
Why do some unfavorable reactions become favorable under cellular conditions
A
Catalysts such and enzymes can make unfavorable reactions favorable under cellular conditions
Remember coupling as well as cascading (le chatliers)
5
Q
What makes a molecule a high energy molecule
A
If it contains a phosphoryl group that is able to be hydrolyzed to release energy
Phosphoric groups generate a large amount of energy due to Resonance Stabilization, Electrostatic Repulsion, Solubility Change
6
Q
what are the chemical thermodynamics of metabolic pathways
A
1 3 and 4 are the irreversible steps of the citric acid cycle
1, 3 and 10 of glycolysis are irreversible
7
Q
how to the chemical thermodynamics make glycolysis favorable
A
Cascading (le chatliers)
8
Q
How does electron movement generate Gibbs free energy
A
breaking of bonds releases the electrons of those bonds making them available to do work
9
Q
What does E’ mean and how does it relate to delta G’
A
E’ is the standard reduction potential of a molecule, i.e. the affinity of a molecule for electrons.
If E’ is Negative this means that electrons are flowing OUT of the testing cell and into the reference cell, i.e. low affinity for electrons in the cell of interest (testing cell)
If E’ is Positive, this means that electrons are flowing INTO the testing cell and OUT of the reference cell, i.e. high affinity for electrons in the cell of interest (testing cell)
∆Gº’ = -nF∆Eº’, therefore if reduction potential is negative, ∆G will be positive and the reaction will be unfavorable. This shows how electrons affect the favorability of a reaction.
10
Q
What is redox potential
A
Reduction potential, also known as E’, is the potential for a molecule to be reduces by electrons. This can be thought of as the molecules affinity for electrons
A positive reduction potential means high electron affinity and a negative reduction potential means low electron affinity.
11
Q
How does redox potential determine the direction of electron flow
A
electrons spontaneously move toward more positive environments
12
Q
what is the functional difference between NAD+ and FAD redox pairs
A
When NAD+ is reduced, the dehydrogenase catalyzing this reaction will release some H+ into surrounding solution.
NAD+ can also only accommodate the addition of one hydrogen atom
FAD can accommodate the addition of 2 hydrogen atoms and none of them get release into solution
13
Q
What vitamins are used to synthesize NAD+ and FAD coenzymes
A
FAD is derived from vitamin B2
NAD+ is derived from vitamin B3
14
Q
What are the steps of glycolysis
A
Step 1: Phosphorylation of Glucose
Step 2: Conversion of Glucose-6-Phosphate to Fructose-6-Phosphate
Step 3: 2nd Priming Phosphorylation
Step 4: Aldol Cleavage of Fructose-1,6-Biphosphate
Step 5: Triose Phosphate Intverconversion (END OF INVESTMENT PHASE)
Step 6: Oxidation of GAP
Step 7: 1st Production of ATP
Step 8: Migration of the Phosphate
Step 9: Dehydration of 2-PG to PEP
Step 10: 2nd Production of ATP
15
Q
What are the steps of glucogenesis
A
Step 1: pyruvate + HCO3- + ATP —-> oxaloacetate + ADP + pi (irreversible)
Step 2: Oxaloacetate + GTP —> phosphoenolpyruvate + CO2 + GDP
Step 3: phosphoenolpyruvate + H2O —> 2-phosphoglycerate
Step 4: 2-phosphoglycerate —> 3-phosphoglycerate
Step 5: 3-phosphoglycerate + ATP —> 1,3 BPG + ADP
Step 6: 1,3 BPG + NADH + H+ —> glyceraldehye 3-phosphate + NAD+ + Pi
Step 7: GAP —> dihydroxyacetone phosphate
Step 8: GAP + DHAP —-> fructose 1,6-bisphosphate
Step 9: fructose 1,6-bisphosphate –> fructose 6-phosphate + Pi (irreversible)
Step 10: fructose 6-phosphate —> glucose 6-phosphate
Step 11: glucose 6-phosphate + H2O —> glucose + Pi (irreversible)
16
Q
what are the steps of lactic acid fermentation
A
Pyruvate gets converted to Lactate or lactic acid by lactate dehydrogenase
in the process of this, NADH is used as a substrate and gets reduced back to NAD+, allowing glycolysis to be performed again
17
Q
substrate, enzymes, and products of step 1 of glycolysis
A
Substrate: Glucose, ATP, Mg2+
Enzyme: Hexokinase
Product: Glucose-6-Phosphate
18
Q
substrate, enzymes, and products of step 2 of glycolysis
A
Substrate: Glucose-6-Phosphate
Enzyme: Phosphohexo isomerase
Product: Fructose-6-Phosphate
19
Q
substrate, enzymes, and products of step 3 of glycolysis
A
Substrate: Fructose-6-Phosphate
Enzyme: Phosphofructokinase-1 (PFK-1)
Product: Fructose-1,6-Biphosphate
20
Q
substrate, enzymes, and products of step 4 of glycolysis
A
Substrate: Fructose 1,6-bisphosphate
Enzyme: aldolase
Product: glyceraldehyde 3-phosphate (GAP) and dihydroxyacetone phosphate (DHAP)
21
Q
substrate, enzymes, and products of step 5 of glycolysis
A
Substrate: dihydroxyacetone phosphate (DHAP)
Enzyme: triose phosphate isomerase
Product: glyceraldehyde 3-phosphate (GAP)
importance: allows glyclolysis to proceed to payoff phase by a single chemical pathway
proceeds via general acid/base catalysis and it is an unfavorable reaction near equilibrium – proceeds in the direction of the prodcuts becuase of the Q value and trickling effect of concentrations from other steps. Based on Le chatliers principle a decreas in [DHAP] pushes forward the production of GAP
22
Q
substrate, enzymes, and products of step 6 of glycolysis
A
Substrate: Glyceraldehyde 3-phosphate + inorganic phosphate + NAD+
Enzyme: glyceraldehyde-3-phosphate dehydrogenase
Product: 1,3 bisphosphoglycerate + NADH + H+
coupled to reaction 7 by product/substrate coupling
23
Q
substrate, enzymes, and products of step 7 of glycolysis
A
Substrate: 1,3-bisphosphoglycerate + ADP
Enzyme: phosphoglycerate kinase + Mg2+
Product: 3-phosphoglycerate + ATP
At this stage net ATP is 0
24
Q
substrate, enzymes, and products of step 8 of glycolysis
A
Substrate: 3-phosphoglycerate
Enzymes: phosphoglycerate mutase + Mg2+
Product: 2-phosphoglycerate
25
substrate, enzymes, and products of step 9 of glycolysis
Substrate: 2-phosphoglycerate
Enzymes: enolase
Product: phosphoenolpyruvate + H2O
26
substrate, enzymes, and products of step 10 of glycolysis
Substrate: phosphoenolpyruvate + ADP
Enzymes: pyruvate kinase + Mg2+, K+
Product: pyruvate + ATP
regulatory point of glycolysis
27
substrate, enzymes, and products of step 1 of the citric acid cycle
Substrate: Acetyl-CoA + Oxaloacetate + H2O
Enzyme: Citrate synthase
Product: Citrate + CoA-SH
delta G: -32.2 kJ/mol; irreversible
28
substrate, enzymes, and products of step 2 of the citric acid cycle
substrate: citrate
Enzyme: aconitase
Product: isocitrate
delta G: 13.3 kJ/mol
happens in 2 parts, first it is dehydrated and forms cis-aconitate, second part is a rehydration resulting in the product
29
substrate, enzymes, and products of step 3 of the citric acid cycle
Substrate: isocitrate + NAD(P)+
enzyme: isocitrate dehydrogenase
Product: alpha-ketoglutarate + NAD(P)H + H+ + CO2
irreversible
30
substrate, enzymes, and products of step 4 of the citric acid cycle
substrate: alpha-ketoglutarate + CoA-SH + NAD+
enzyme: a-ketoglutarate dehydrogenase complex
Product: Succinyl-CoA + NADH + CO2
delta G: -33.5 kJ/mol; irreversible
31
substrate, enzymes, and products of step 5 of the citric acid cycle
Substrate: succinyl-CoA + GDP+Pi
enzyme: succinyl-CoA synthetase
product: succinate + GTP + CoA-SH
delta G: -2.9 kJ/mol
32
substrate, enzymes, and products of step 6 of the citric acid cycle
substrate: succinate + FAD
enzyme: succinate dehydrogenase
Product: fumarate + FADH2
delt G: 0 kJ/mol
33
substrate, enzymes, and products of step 7 of the citric acid cycle
substrate: fumarate
enzyme: fumarase
product: L-malate
delta G: -3.8 kJ/mol
34
substrate, enzymes, and products of step 8 of the citric acid cycle
substrate: L-malate + NAD+
enzyme: L-malate dehydrogenase
Product: oxaloacetate + NADH+H+
delta G: 29.7 kJ/mol
35
What does kinase do
Addition of a phosphate group to a molecule. Requires nucleotide.
36
what does phosphatase do
Removal of a phosphate group from a protein
37
what does dehydrogenase do
Transfer 2 hydrogen atoms from organic compounds to electron acceptors. This oxidizes the organic compound and creates energy (because of the liberation of electrons for energy use right?)
38
what does mutase do
An isomerase that catalyzes the movement of a functional group from one to another within the same molecule
i.e. catalyzes INTRAmolecular group transfers
39
what does isomerase do
Catalyze changes within a molecule to change one isomer into another
40
what does enolase do
Reversibly converts 2PG to PEP in step 9 of glycolysis
41
what does aldolase do
Breaks down certain sugars to produce energy
e.g. in step 4 of glycolysis, Fructose-1,6-biphosphate is converted into dihydroxyacetone and glyceraldehyde-3-phosphate via and aldolase
42
what does carboxylase do
Catalyze the incorporation of a CO2 molecule into an organic substrate
43
where in the cell does glycolysis occur
The cytoplasm
44
where in the body does gluconeogenesis occur
The liver and the kidneys
45
where in the body does glycolysis occur
glycolysis occurs in all cells
46
where in the cell does gluconeogenesis occur
The mitochondria or cytoplasm depending on the substrate being used
47
where in the cell does lactic acid fermentation occur
The cytoplasm
48
where in the body does lactic acid fermentation occur
Skeletal muscles
49
what is the mechanism for step 2 of glycolysis
what is the importance of this step in the glycolytic pathway
Step 2 turns glucose 6-phosphate (aldose) into fructose 6-phosphate (ketose) via the isomerization of glucose 6-phosphate (catalyzed by phosphoglucose isomerase). The rearrangement moves the beta bond, traps the glucose, and prevents water from hydrolyzing ATP. The beta bond is more reactive and sets the stage to produce 2 trioses via phosphorylation.
50
what is the mechanism of step 4 of glycolysis
what is the importance of this step in the glycolytic pathway
Frucotse 1,6-bisphosphate is brokendown into 3 carbon molecules: glyceraldehyde 3-phosohate (GAP) and dihydroxyacetone phosphate (DHAP). GAP can go fireclty to the next step, but DHAP must be modified before it can be used. Triose phosphate isomerase catalyzes the conversion of DHAP to GAP via an intramolecular redox reaction where an H is transferred from carbon 1 to carbon 2. Le chateliers principle keeep sto conversion going as GAP keeps getting pulled into the next step it must keep transforming DHAP (decrease in [DHAP] pushes forward production of GAP).
This is thermodynamically unfavorable BUT IT DOES NOT REQUIRE ATP becuase what is happening with molar concentrations before and after this step causes a shift making le chateliers principle favor prodcuts, pushing glycolysis forward with no extra energy investment
51
what is the mechanism of step 6 of glycolysis
what is the importance of this step in the glycolytic pathway
GAP is oxidized and phosphorylated to form 1,3-bisphosphoglycerate. This is the ONLY redox reaction seen in the glycolytic pathway. This step results in the production of 2 high energy intermediates (1,3-BPG and NADH).
The energy to transfer a phosphate group comes from the changing concentrations and electron movement during the redox reaction (redox rxn creates free energy).
52
what is the mechanism of step 8 of glycolysis
what is the importance of this step in the glycolytic pathway
3-phosphoglycerate is isomerized into 2-phosphogylcerate to prepare for step 9. The isomerization occurs via rearrangement. The enzyme is phosphoglycerate mutase, whihc requires Mg2+. This isomerization is important because it prepares the mechanism for an alpha beta elimination.
(she didn't ask/say this but I feel like she could ask its relation to 2,3-BPG: this reaction requires catalytic amounts of 2,3-BPG. 2,3-BPG is used to keep catalytic histidine residue in its active phosphorylated state. The histidine removes the phosphoryl group from the third carbon)
53
why does reaction 6 of the glycolysis require no energy from ATP to proceed toward products (Compare gibbs free energy under standard conditions and under the reaction in this cell)
Because reaction 6 is coupled to reaction 7 by product substrate coupling
its the only redox reaction seen in the glycolytic pathway. Redox reaction creates electron movement which creates free energy.
54
what reactions are different in gluconeogenesis
Steps 1, 3, and 10 of glycolysis are irreversible. This means that gluconeogenesis cannot simply perform these reactions in reverse but must find alternative ways of synthesizing the molecules.
In steps 1, 3 and 10 a different enzyme is used to make the reverse reactions favorable and possible in gluconeogenesis.
Step 1 (i.e. step 11): Enzyme glucose 6 phosphatase and water remove a phosphate group from glucose-6-phosphate to yield glucose.
In step 3 (i.e. step 8): Enzyme fructose-1,6-bisphosphatase and water are used to remove a phosphate group from Fructose-1,6-bisphosphate to yield Fructose-6-phosphate
In step 10 (i.e. step 1/2): Enzyme pyruvate carboxylase and biotin are used to convert pyruvate (product of glycolysis) into oxaloacetate and ADP. Some intermediate steps occur and then enzyme PEP carboxykinase uses oxaloacetate and GTP to produce GDP and PEP
55
why cant the reactions in gluconeogenesis just use a reverse glycolytic enzyme
Some of the reaction are irreversible and gluconeogenesis needs to bypass this.
56
what is lactic acid fermentation and why is it important
Lactic acid fermentation is the process that converts pyruvate (product of glycolysis) into lactic acid or lactate via lactate dehydrogenase. In this reaction NADH (another product of glycolysis) is used as a substrate and thus oxidized back to NAD+ (substrate of glycolysis) so that the glycolysis process can begin again to produce more ATP
This is important because this is the system that kicks into place when oxygen is absent the citric acid cycle is unable to be initiated following glycolysis. The citric acid cycle yields the main production of ATP and although Glycolysis does not produce as much ATP as the citric acid cycle, it is better than none
57
what is the net equation for glycolysis under aerobic state
glucose + 2 Pi + 2 ADP + 2 NAD+ ----> 2 pyruvate + 2 ATP + 2 NADH + 2 H2O + 2 H+
58
how is PFK and bisphosphatase coordinately regulated; include insulin and glucagon regulation
im waiting to answer this bc the girl next to me said Dr. lahousse said we dont need to know about insulin and glucagon but i dont trust dr. lahousse
59
what is the net reaction for glycolysis under anaerobic conditions
glucose + 2ADP + 2 Pi --> 2 lactate + 2 ATP + 2 H2O
60
what is the net equation for gluconeogenesis
2 pyruvate + 4 ATP + 2 GTP + 2 NADH +2H+ + 4 H20 --> glucose + 4 ADP + 2 GDP + 6 Pi + 2 NAD+
costs 4 ATP, 2 GTP, and 2 NADH
61
how is pyruvate converted to acetyl-CoA for entry into the citric acid cycle (prepatory step for the citric acid cylce). What enzyme is regulated via covalent modification
**Step 1.** Pyruvate reacts with the bound thiamine pyrophosphate (TPP) of pyruvate dehydrogenase (E1), undergoing decarboxylation to from hydroxyethyl derivative of thiazole ring of TPP.
**Step 2**. Pyruvate dehydrogenase transfers two electrons and the acetyl group from TPP to the oxidized form of the lipoyllysyl group of the core enzyme, dihydrolipoyl transacetylase (E2), to form the acetyl thioester of the reduced lipoyl group.
**Step 3.** It is a transesterification process in which the —SH group of CoA replaces the—SH group of E2 to yield acetyl-CoA and the fully reduced (dithiol) form of the lipoyl group.
**Step 4**. Dihydrolipoyl dehydrogenase (E3) promotes transfer of two hydrogen atoms from the reduced lipoyl groups of E2 to the FAD prosthetic group of E3, restoring the oxidized form of the lipoyllysyl group of E2.
**Step 5**. The reduced FADH2 of E3 transfers a hydride ion to NAD+, forming NADH. The enzyme complex is now ready for another catalytic cycle.
Note: Coenzyme A (CoA) is an organic molecule derived from vitamin B5, to form acetyl CoA.
**Catalyzed via the pyruvate dehydrogenase complex (PDH)**, which uses 5 coenzymes: TPP, Lipoic acid, CoA, FAD, and NAD+
Lipoic acid is covalently linked to a Lys on lipoamide
**Advantages:**
1. diffusion distance: very short distance between enzymes - makes diffusion really fast
2. minimizes side reactions (due to proximity
3. cordinated control of reactions - reuglating one enzyme regulates teh entire process
**Regulation:**
**End-product inhibition:**
- Pyruvate dehydrogenase is a good example for end product (acetyl CoA, NADH) inhibition.
- Acetyl-CoA and NADH, both end products of the pyruvate dehydrogenase reaction, are potent allosteric inhibitors of the enzyme.
- The inhibitory effects are reversed on the addition of coenzyme A and NAD+ respectively.
**Feedback regulation:**
- The activity of PDC is controlled by the energy charge.
- The pyruvate dehydrogenase component is specifically inhibited by GTP or ATP and activated by AMP.
**Covalent modification.**
- Under conditions of high concentrations of ATP, acetyl-CoA, and those of the intermediates of TCA cycle, further formation of acetyl-CoA is slowed down.
- This is accomplished by covalent modification.
- PDH is regulated by phosphorylation and dephosphorylation.
- PDH is active as a dephosphoenzyme while it is inactive as a phosphoenzyme.
- PDH kinase (responsible to form inactive PDH) is promoted by ATP, NADH, and acetyl CoA, while it is inhibited by NAD+, CoA, and pyruvate.
- PDH activity is promoted by Ca2+ ,Mg2+ and insulin(in adipose tissue).
- Calcium released during muscle contraction stimulates PDH (by increasing phosphatase activity) for energy Production.
- The net result is that in the presence of high energy signals (ATP, NADH), the PDH is turned off.
62
what are the steps of the citric acid cycle (general overview)
Step 1: Formation of citrate (irreversible)
Step 2: formation of isocitrate
Step 3: oxidative decarboxylation of isocitrate (irreversible)
Step 4: oxidation-decarboxylation reaction of α-ketoglutarate (irreversible)
Step 5: formation of succinate
Step 6: oxidation of succinate
Step 7: hydration of fumurate
Step 8: oxidation of malate
63
what substrates, enzymes, and products are involved in step 1 of the citric acid cycle
what are the thermodynamics of this step
formation of citrate
acetyl-CoA donates its 2- carbon acetyl group 4-carbon to oxaloacetate, forming 6-carbon citrate. Note that anytime a molecule is bound to coenzyme A, it is bound by a thioester bond. Hydrolysis of a thioester bond is highly exergonic and releases a high amount of free energy. This reaction is essential for driving many endergonic or unfavorable processes. In this instance, it is helpful because the oxaloacetate concentration in the mitochondrial matrix is relatively low, and the highly exergonic hydrolysis of the thioester bond helps to push the unfavorable addition reaction forward.
oxaloacetate is the first to bind, conformational changes create the binding site for acetyl-coa. Once citroyl is formed, conformational change breaks thioester bond via general acid base catalysis
Substrate: acetyl CoA and oxaloacetate. Citric acid cylce will not start without oxaloactetate. presence of acetyl coa allows for the condensation to take place even wen concentration of oxalocetate is low
Enzyme: citrate synthase
Product: citrate
Thermodynamics: -32.2 kJ/mol (favorable reaction). This step is **irreversible **and a regulatory step in the pathway
64
what substrates, enzymes, and products are involved in step 2 of the citric acid cycle
what are the thermodynamics of this step
formation of isocitrate
two-step reaction: citrate is isomerized to isocitrate. In the first step of this reaction, a dehydration reaction results in cis-aconitate formation from citrate. The subsequent reaction is a hydration reaction, forming isocitrate from cis-aconitate. (first removal then addition of water molecule)
Substrate: citrate
Enzyme: aconitase
Product: isocitrate
Thermodynamics: unfavobrable under standard conditions but reaction is pulled forward by step 2
65
what substrates, enzymes, and products are involved in step 3 of the citric acid cycle
what are the thermodynamics of this step
oxidative decarboxylation of isocitrate
isocitrate is oxidized and decarboxylated to form α-ketoglutarate and carbon dioxide. Note that one of the carbons from the acetyl group of isocitrate and acetyl-CoA is released as carbon dioxide, making α-ketoglutarate a 5-carbon molecule. Also, as isocitrate is oxidized, NAD+ is reduced to NADH. The NADH will be shuttled to the electron transport chain to donate the energy has captured towards ATP production.
2 step process: step 1: isocitrate dehydrogenized into oxalosuccinate (intermediate); NAD+ is reduced. Step 2: decarboxylation of oxalosuccinate into α-ketoglutarate
Substrate: isocitrate
Enzyme: isocitrate dehydrogenase
Product: α-ketoglutarate
Thermodynamics: delta G': -11.6 kJ/mol. **This step is irreversible and a major regulatory step in the citric acid cycle**
also Mn2+ is in the active site to stabilize the carbonyl of oxalosuccinate intermediate. **Mg2+ or Mn2+ are required cofactors besides NAD+**
66
what substrates, enzymes, and products are involved in step 4 of the citric acid cycle
what are the thermodynamics of this step
oxidation-decarboxylation reaction. α-ketoglutarate is oxidized and decarboxylated to form four-carbon succinyl-CoA and carbon dioxide, and NAD+ is reduced to NADH. Also, note the addition of CoA-SH to form succinyl-CoA.
Substrate: α-ketoglutarate
Enzyme: α-ketoglutarate dehydrogenase complex
Product: succinyl-CoA (high energy compound)
Thermodynamics: Delta G': -33.5kJ/mol,** irreversible**, energy of oxidation is conserved in formation of thioester to CoA.
In this step: coenzyme A is added, CO2 is removed, and NAD+ is reduced forming NADH and H+
also note: multienzyme complex that looks and functions similar to pyruvate dehydrogenase (she had this on her slides)
67
what substrates, enzymes, and products are involved in step 5 of the citric acid cycle
what are the thermodynamics of this step
At this point in the cycle, two carbons have been removed from acetyl-CoA as carbon dioxide, thus essentially completing the oxidation of glucose. Therefore, steps 5-8 essentially serve to regenerate oxaloacetate so that another cycle can take place. In the fifth step, succinate is formed by hydrolyzing the thioester bond of succinyl-CoA (breaking of a thioester bond is highly exergonic can be coupled to an endergonic reaction.) In this step, the endergonic reaction performed is the formation of GTP from GDP by substrate-level phosphorylation. This entire reaction is catalyzed by the enzyme succinyl-CoA synthetase.
Substrate: Succinyl CoA (can be ADP or GDP)
Enzyme: sccinyl-CoA synthetase
Prodcut: GTP
Thermodynamics: thioester succinyl-CoA releases a large amount of free energy when hydrolyzed (drives synthesis of nucleoside triphosphate from nucleodisphosphate and Pi) - **endergonic reaction **
-substrate level phosphorylation: **exergonic reaction coupled to the transfer of a phsophoryl group to nucleoside diphosphate**
-series of phosphoryl group transfers that involve an active His residue
- catalyzes substrate level phosphorylation
- overall delta G: -2.9 kJ/mol (I think)
68
what substrates, enzymes, and products are involved in step 6 of the citric acid cycle
what are the thermodynamics of this step
succinate is oxidized to fumarate and FAD is reduced to FADH2
Substrates: succinate
Enzyme: succinate dehydrogenase
Products: Fumarate
-generates ubiquinol (lipid soluble)
-succinate dehydrogenase catalyzes the reversible dehydrogenation of succinate to fumarate
-embedded in inner mitochondrial membrane
Thermodynamics: delta G': -11.6 kJ/mol
One important thing to note is that succinate dehydrogenase is the only enzyme of the Krebs cycle that participates in both the Krebs cycle and the electron transport chain.
69
what substrates, enzymes, and products are involved in step 7 of the citric acid cycle
what are the thermodynamics of this step
hydration of fumarate
-catalyzes hydration reaction
-reversible hydration of double bond to convert fumarate to malate
Substrate: Fumarate
Enzyme: fumarase
Product: Malate
thermodynamics: not mentioned if you can find it plz add it but I think it is irrelevant
70
what substrates, enzymes, and products are involved in step 8 of the citric acid cycle
what are the thermodynamic of this step
oxaloacetate is regenerated by oxidation of malate. Another molecule of NAD+ is reduced to NADH in the process. the Krebs cycle starts with the generation of oxaloacetate and ends with its regeneration. In this way, as long as acetyl-CoA is present in the body, the Krebs cycle will run continuously.
Substrate: L-Malate
Enzyme: Malate dehydrogenase
Product: Oxaloacetate
Thermodynamics: delta G': +29.7 kJ/mol; only continues because the next step in the cycle is highly exergonic which pulls reaction forward
71
what are the most important steps in the citric acid cycle and why
The irreversible steps of the citric acid cycle are steps 1,3, and 4
Prior to step one pyruvate oxidation must occur
Step One: This is a condensation step, combining the two-carbon acetyl group with a four-carbon oxaloacetate molecule to form a six-carbon molecule of citrate. CoA is bound to a sulfhydryl group (-SH) and diffuses away to eventually combine with another acetyl group. This step is irreversible because it is highly exergonic. The rate of this reaction is controlled by negative feedback and the amount of ATP available. If ATP levels increase, the rate of this reaction decreases. If ATP is in short supply, the rate increases.
Step 3: isocitrate is oxidized, producing a five-carbon molecule, α-ketoglutarate, together with a molecule of CO2 and two electrons, which reduce NAD+ to NADH. This step is also regulated by negative feedback from ATP and NADH, and a positive effect of ADP.
Steps 3 and 4: Steps three and four are both oxidation and decarboxylation steps, which release electrons that reduce NAD+ to NADH and release carboxyl groups that form CO2 molecules.** α-Ketoglutarate is the product of step three, and a succinyl group is the product of step four.** CoA binds the succinyl group to form succinyl CoA. The enzyme that catalyzes step four is regulated by feedback inhibition of ATP, succinyl CoA, and NADH.
72
what is the amino acid point of entry in the citric acid cycle
Each amino acid must have its amino group removed (deamination) prior to the carbon chain’s entry into the pathways. When the amino group is removed from an amino acid, it is converted into ammonia through the urea cycle. The remaining atoms of the amino acid result in a keto acid. The keto acid can then enter the citric acid cycle. When deaminated, **amino acids can enter the pathways of glucose metabolism as pyruvate, acetyl CoA, or several components of the citric acid cycle** Several amino acids can enter glucose catabolism at multiple locations.
73
what are the points of control in the citric acid cycle and what molecules function as regulators
the citric acid cycle is controlled through the enzymes that break down the reactions that make the first two molecules of NADH.
**Step One:** **Citrate synthase** is responsible for the rate of reaction in the first step of the cycle when the acetyl-CoA is combined with oxaloacetic acid to form citrate. It is inhibited by high concentrations of ATP, acetyl-CoA, and NADH which indicates an already high level of energy supply. The molecule produced in the reaction, citrate, can also act as an inhibitor of the reaction. Because citrate synthase is inhibited by the final product of the citric acid cycle as ATP, ADP works as an allosteric activator of the enzyme as ATP is formed from ADP. Therefore, the rate of the cycle is reduced when the cell has a high level of ATP.
**Step Three**: The enzyme** isocitrate dehydrogenase** is an important catalyst in the third step of the reaction. It regulates the speed at which the citrate isomer isocitrate loses a carbon to form the five-carbon molecule α-ketoglutarate. The coenzyme NADH is a product of the reaction and, at high levels, acts as an inhibitor by directly displacing the NAD+ molecules it is formed from.
**Step 4**: The enzyme **α-ketoglutarate dehydrogenase** is another important catalyst in the fourth step of the cycle where α-ketoglutarate also loses a carbon and combines with Coenzyme A to form succinyl CoA. The two products of the reaction, succinyl CoA and NADH, both work as inhibitors at large concentrations.
The 3 forms of control are: substrate concentration, product inhibition, and feedback inhibition
after looking through the slides she may be looking for something different so i might make a second card explaining that
74
why is the citric acid cycle also known as cellular respiration
this is a stupid question because the citric acid cycle is not known as cellular respiration. The combo of glycolysis, the citric acid cycle, and the electron transport chain are known as cellular respiration. ANYWAYS it's because cell seems to “respire” in a way that it takes in molecular oxygen (as an electron acceptor) and releases carbon dioxide (as an end product).
75
what is the function of O2 in cellular respiration
Oxygen serves as a final electron acceptor of the ETC in cellular respiration, facilitating the movement of electrons down a chain, resulting in the synthesis of ATP. Oxygen combines with electrons and hydrogen ions to produce water. The electron transport chain is directly dependent on oxygen. The oxygen that is used in cellular respiration comes from breathing. This process occurs in the inner mitochondrial membrane and matrix in eukaryotic cells.
76
How many ATP molecules can be synthesized from NADH and FADH when they are sent to the electron transport chain
oxidation of one molecule of NADH leads to the production of three molecules of ATP
oxidation of FADH2 produces 2 ATP molecules
77
what is the function of the electron transport chain
To generate an electrochemical gradient that drives the synthesis of ATP during cellular respiration and photosynthesis
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why would the citric acid stop with no oxygen
Without oxygen there is no way to regenerate the NAD+ used in the process.
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how is the electron transport chain connected to the synthesis of ATP
The ETC transfer electrons via REDOX reactions and couples the electron transfer with transfer of protons across a membrane. Together, this creates an electrochemical transport gradient that drives the synthesis of ATP.
Electron transport chains are used for extracting energy via redox reactions from sunlight in photosynthesis or, such as in the case of the oxidation of sugars, cellular respiration. In eukaryotes, an important electron transport chain is found in the inner mitochondrial membrane where it serves as the site of oxidative phosphorylation through the action of ATP synthase.
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what is the funtion of Thiamine Pyrophosphate (TPP) in PDH
Bound to E1
decarboxylates pyruvate, yielding a hydroxyethyl-TPP carbanion
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what is the funtion of Lipoic Acid in PDH
location: covalently linked to a Lys on E2 (lipoamide)
Function: accepts the hydroxyethyl carbanion from TPP as an acetyl group
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what is the funtion of Coenzyme A (CoA) in PDH
location: substrate for E2
Function: accepts the acetyl group from lipoamide
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what is the funtion of Flavin adenine dinucleotide (FAD) in PDH
location: bound to E3
function: reduced by lipoamide
it facilitates the transfer of electrons since 2 electrons need transferred
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what is the funtion of Nicotinamide adenine dinucleotide (NAD+) in PDH
location: substrate for E3
function: reduced by FADH2
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what is the difference between complex I and complex II relating to NADH and FADH2
In the matrix, NADH deposits electrons at Complex I, turning into NAD+ and releasing a proton into the matrix. FADH2 in the matrix deposits electrons at Complex II, turning into FAD and releasing 2 H+.
Complex I results in the production of 4 protons where as complex II does not transfer any protons so it does not contribute to the proton gradient
2 ATPs are generated from FADH2 and 3 ATPs are obtained from NADH + H+ .
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How is complex II of the ETC related to step 6 of TCA
E-FADH2 is a membrane bound enzyme and represents complex II of the the ETC for oxidative respiration (Coenzyme Q)
Idk wtf E-FADH2 is but succinate dehydrogenase is attached to innermembrane matrix and it takes FAD and reduces it to FAHD2. Electrons from FADH2, formed in step 6 of the citric acid cycle, enter the electron transport chain through complex II.
