Chapter 8 - Metabolic Pathways Flashcards
What is the most common enzyme that makes use of glucose when it enters the cell?
hexokinase
What is a kinase?
an enzyme that involves the transfer of a terminal phosphate group of an ATP unit to some other compound
In glycolysis, what happens to glucose (Step 1)?
Step 1 (first investment step): glucose is converted to glucose-6-phosphate with the help of hexokinase which transfers a phosphate from ATP to the C6 position.
What is the significance of phophorylating glucose once it is inside the cell?
Adding a negative charge from the phosphate group traps glucose in the cell. It cannot pass through the cell membrane.
In glycolysis, what happens to glucose-6-phosphate?
Step 2: glucose-6-phosphate is isomerized into fructose-6-phosphate by the enzyme phosphoglucose isomerase.
*enediol intermediate
In glycolysis, what happens to fructose-6-phosphate?
Step 3 (second investment step): fructose-6-phosphate is converted to fructose-1,6-diphosphate by a transferase, phosphofructokinase, which transfers a phosphate from ATP to the C1 position.
In glycolysis, what happens to fructose-1,6-diphosphate?
Step 4: fructose-1,6-diphosphate is cleaved by a lyase, aldolase between C3 and C4 to form dihydroxyacetonephosphate (DHAP) and glyceraldehyde 3-phosphate (G3P).
*Reverse aldol condensation
In glycolysis, what happens to dihydroxyacetonephosphate (DHAP)?
Step 5: dihydroxyacetonephosphate (DHAP) is isomerized into glyceraldehyde-3-phosphate (G3P) by triose phosphate isomerase.
Describe Phase I of glycolysis (final products, what has been used)
Glucose is converted into two triose phosphates (G3P). There has been no oxidation/reduction. 2 ATP have been used.
In glycolysis, what happens to glyceraldehyde-3-phosphate (G3P)?
Step 6: glyceraldehyde-3-phosphate (G3P) is converted to 1,3-diphosphoglycerate (1,3-DPG) by glyceraldehyde-3-phosphate dehydrogenase, which uses NAD+ to oxidize the C1 position and adds a phosphate from Pi.
In glycolysis, what happens to 1,3-diphosphoglycerate?
Step 7: 1,3-diphosphoglycerate is converted to 3-phosphoglycerate by phosphoglycerate kinase, which transfers a phosphate to ADP to form ATP.
In glycolysis, what happens to 3-phosphoglycerate?
Step 8: 3-phosphoglycerate is converted to 2-phosphoglycerate by phosphoglyceromutase, which exchanges the current phosphate for a phosphate on the enzyme.
In glycolysis, what happens to 2-phosphoglycerate? What is a side reaction?
Step 9: 2-phosphoglycerate is converted to phosphoenolpyruvate (PEP) by enolase.
*2-phosphoglycerate can also be converted to 2,3-bisphosphoglycerate (2,3-BPG) by 2,3-BPG phosphatase.
In glycolysis, what happens to phosphoenolpyruvate (PEP)?
Step 10: phosphoenolpyruvate (PEP) is converted to pyruvate by pyruvate kinase, which transfers a phosphate group to ADP to form ATP.
In which ways can NAD+/FAD be regenerated after glycolysis?
Anaerobic conditions: pyruvate can be converted to lactate by lactace dehydrogenase, which uses NADH to reduce pyruvate, forming NAD+.
Yeasts (alcoholic fermentation): pyruvate can be converted to acetaldehyde by the lyase, pyruvate decarboxylase and then to ethanol by alcohol dehydrogenase, which uses NADH to reduce acetaldehyde, forming NAD+.
*Aerobic conditions: pyruvate is oxidized to carbon dioxide through the Krebs cycle, producing more NADH and FADH2. Those lost electrons are eventually shuttled to oxygen on the electron transport chain, regenerating NAD+ and FAD.
What is the most important regulatory step in glycolysis? What are 3 examples of inhibition at this step?
Regulation is important at step 3. Phosphofructokinase is inhibited by high levels of ATP, H+ (from formation of lactate), and citrate (Krebs cycle). These signifiy that glucose is being used well, and shouldn’t be wasted.
What hydrolytic enzymes break down disaccharides in the small intestine?
maltase, sucrase, and lactase (sometimes)
How can monosaccharides other than glucose be used for glycolysis?
They must be converted to an intermediate in the glycolytic pathway.
Where does glycolysis occur in the cell?
cytosol
Where does the Krebs/citric acid cycle occur in the cell?
mitochondrial matrix
What is the first major reaction pyruvate undergoes in its journey to the Krebs cycle?
Pyruvate is decarboxylated by a pyruvate dehydrogenase complex (3 enzymes) to form acetyl-coenzyme A and carbon dioxide. This step is accompanied by NAD+ which reduces to NADH.
How is acetyl coenzyme A introduced to the Krebs cycle?
It is undergoes an aldol condensation and hydrolysis with oxaloacetic acid to form citrate and releases coenzyme A. The lyase, citrate synthetase carries out this reaction.
What is the unique functional group in acetyl-coenzyme A and succinyl-coenzyme A?
They have a high energy thioester bond.
What is a lyase?
an enzyme that catalyzes the breaking of bonds by means other than hydrolysis and oxidation, often forming a new double bond or ring structure
In the Krebs cycle, what happens to citrate?
Citrate loses its hydroxyl group with the help of aconitase, forming a tertiarty carbonium ion intermediate. An elimination reaction makes cis-Aconitate than can then be hydrolyzed with the help of aconitase to form isocitrate.
In the Krebs cycle, what happens to isocitrate?
Isocitrate is oxidized by NAD+ with isocitrate dehydrogenase to form a β-keto acid that is very unstable, with the release of NADH. It decarboxylates, forming α-ketoglutarate (α-KG) and releases carbon dioxide.
In the Krebs cycle, what happens to α-ketoglutarate?
α-ketoglutarate will be oxidized by NAD+ with the help of an α-Ketoglutarate Dehydrogenase Complex, forming succinyl-coenzyme A, with the release of NADH and carbon dioxide.
In the Krebs cycle, what happens to succinyl-coenzyme A?
Succinyl-coenzyme A is converted to succinate by a ligase, succinyl-coA synthetase, which uses the water produced from the synthesis of GTP from GDP and Pi to hydrolyze the thioester bond. GTP and coenzyme A are released.
What is a ligase?
an enzyme that puts two molecules together using a high energy phosphate bond
In the Krebs cycle, what happens to succinate?
Succinate is oxidized to fumerate by FAD, with the help of succinate dehydrogenase.
In metabolism, NAD normally converts what to what?
It normally oxidized alcohols to ketones/aldehydes.
In metabolism, FAD normally converts what to what?
It typically oxidizes alkanes to alkenes.
In the Krebs cycle, what happens to fumarate?
Fumarate reacts with water to produce malate, with the help of a lyase, fumarase.
In the Krebs cycle, what happens to malate?
Malate is oxidized to oxaloacetic acid by NAD+ with the help of malate dehydrogenase.
In the Krebs cycle, what happens to oxaloacetic acid?
Oxaloacetic acid undergoes an aldol condensation and hydrolysis with acetyl-coenzyme A to form citrate, with the help of a lyase, citrate synthetase. Coenzyme A is released.
What is the “potential energy” generated in the Krebs cycle?
Many reduced coenzymes (FADH2 and NADH) have been made, which can later be oxidized by oxygen to liberate a lot of energy.
Is the Krebs cycle catabolic or anabolic? Why?
It is catabolic because acetyl coenzyme A is broken down to release 2 of its carbons in the form of carbon dioxide.
Describe the thermodynamics of the Krebs cycle
It has a favorable, negative ΔGº because carbon dioxide is released as a gas. It is very difficult to harness that for the reverse process.
Is glycolysis oxidative or reductive overall?
It is oxidative.
Is the Krebs cycle oxidative or reductive overall?
It is oxidative.
What is the final electron acceptor/oxidizing agent? What does it produce?
Oxygen (O2) - it is reduced to 2H2O by picking up 4 hydrogens and 4 electrons.
What is the space between the inner and outer mitochondrial membranes?
intermembrane space
What is the space within the inner mitochondrial membrane?
matrix
How does the concentration of protons differ between the intermembrane space and the matrix of mitochondria?
Their concentration is much higher in the intermembrane space.
Where do electron transport and oxidative phosphorylation occur?
on the inner membrane of the mitochondria
What is the membrane permeability difference between the inner and outer membranes of mitochondria?
The outer membrane is much more permeable to substances than the inner membrane.
Where do oxidative phosphorylation and electron transport occur in prokaryotes?
on their inner cytoplasmic membrane
Where does the Krebs cycle occur in prokaryotes?
cytoplasm
In the electron transport chain, what are Complex I-IV called?
respiratory chain
In the electron transport chain, what occurs at Complex I (NADH-Q-reductase)?
NADH passes 2 electrons and 2 hydrogens to the FMN prosthetic group in the protein complex, regenerating NAD+. The electrons are then passed to the quinone, coenzyme Q.
In the electron transport chain, what occurs at Complex II (Succinate-Q-reductase)?
FADH2 passes its electrons to the Fe-S prosthetic group associated with the complex, regenerating FAD. The electrons are then passed to the quinone, coenzyme Q.
In the electron transport chain, what occurs after coenzyme Q is reduced?
It passes its electrons to Complex III (Cytochrome reductase) which has cytochromes b and c.
In the electron transport chain, what happens after cytochrome c is reduced?
It passes its electrons to Complex IV (cytochrome oxidase), which has heme groups a and a3. The electrons are then passed to oxygen, forming water.
In oxidative phosphorylation, how many ATP are generated for every NADH and FADH2 in the ETC (P/O ratio)?
NADH: 3 ATP
FADH2: 2 ATP (enters ETC late)
What is substrate-level phosphorylation compared to oxidative phosphorylation?
Substrate-level phosphorylation refers to the 6 high energy phosphate bonds formed during glycolysis and the Krebs cycle. They did not depend on the presence of oxygen, whereas the ATP made in oxidative phosphorylation do.
Describe the chemiosmotic hypothesis
ATP synthesis and the ETC are coupled together by a proton gradient that establishes itself across the inner mitochondrial membrane. The coupling factor is the ATPase that synthesizes ATP using the free energy released as a proton passes through it from the intermembrane space to the matrix.
How is the proton gradient established across the inner mitochondrial membrane?
As the protein complexes are reduced and oxidized with the transfer of electrons, hydrogen ions are removed from the matrix and pumped into the intermembrane space.
What would happen if hydrogen could easily pass back through the inner membrane to the matrix?
The electron transport-ATP production would become uncoupled and all chemical energy would be lost as heat.
How does transport of NADH from the cytosol to the mitochondrial matrix affect ATP production?
The 2 NADH from glycolysis must be transported. If the malate-aspartate shuttle is used, 3 ATP can be made from 1 NADH. If the glycerol-phosphate shuttle is used, 2 ATP can be made from 1 NADH. This is why there are 36-38 ATP made in cellular respiration.
What is the thermodynamic efficiency for complete oxidation of glucose?
~40%
What is the effect of rotenone, antimycin A, cyanide, azide, or carbon monoxide on cellular respiration?
They all inhibit parts of the ETC.
What is the purpose of the pentose phosphate pathways?
It generates reducing power in the form of NADPH and five carbon sugars.
What coenzyme is involved in anabolic mechanisms?
NADP
What is the Cori cycle?
Lactate in the liver can be converted back to pyruvate and then glucose through gluconeogenesis. That glucose can then leave the liver and undergo glycolysis in the skeletal muscle where it can be converted to lactate.
What molecules can be converted to glucose through gluconeogenesis?
- lactate
- glucogenic amino acids (only those with 3 carbons)
- glycerol
*these are all 3-carbon molecules! We do not have the enzymes to convert smaller molecules into glucose.
How many ATP are used in gluconeogenesis?
6 ATP
In gluconeogenesis, what happens to pyruvate after it is made from lactate? What activates the enzyme that carries out this reaction? Why?
Pyruvate diffuses into the mitochondrial matrix and is carboxylated by a ligase, pyruvate carboxylase to form oxaloacetic acid. An ATP is used, releasing ADP and Pi.
Pyruvate carboxylase is activated by high levels of acetyl-coenzyme A. Oxaloacetic acid can then react in with acetyl-coA in the Krebs cycle if ATP is low to form more ATP, or it can be utilized for gluconeogensis if ATP is high.
In gluconeogenesis within the mitochondrial matrix, what happens to oxaloacetic acid?
It is reduced to malate by NADH and the oxidoreductase, malate dehydrogenase, releasing NAD+.
In gluconeogenesis, what happens to malate?
It is transported to the cytosol where it is oxidized to oxaloacetic acid by NAD+ and the oxidoreductase, malate dehydrogenase. NADH is released.
In gluconeogenesis within the cytosol, what happens to oxaloacetic acid?
It is decarboxylated and phosphorylated by GTP and PEP carboxykinase to give phosphoenolpyruvate (PEP), releasing GDP and CO2.
In gluconeogenesis, what happens to phosphoenolpyruvate (PEP)? How is it prevented from forming pyruvate like it did in glycolysis?
It will undergo reversible reactions in glycolysis until it becomes fructose-1,6-diphosphate.
This will only happen at high levels of ATP because high levels of ATP allosterically inhibit pyruvate kinase, the enzyme that converts PEP to pyruvate.
In gluconeogenesis, what happens to fructose-1,6-diphosphate?
It is hydrolyzed by water and the hydrolase, fructose-1,6-diphosphate phosphatase to form fructose-6-phosphate.
In gluconeogenesis, what happens to fructose-6-phosphate?
It is hydrolyzed by water and glucose-6-phosphate phosphatase to form glucose.
Structurally, why is there more energy available in triglycerides than glycogen?
The fatty acids of triglycerides has more reduced groups than carbohydrates: CH2 vs. CHOH.
This means that fats have a greater ability to be oxidized.
What is the first step in fatty acid oxidation?
Triglycerides are hydrolyzed by water and lipase into glycerol and 3 fatty acid residues.
In fatty acid oxidation, what happens to glycerol?
It is converted to glycerol-3-phosphate by glycerol kinase and ATP, releasing ADP.
In fatty acid oxidation, what happens to glycerol-3-phosphate?
It is converted to dihydroxyacetone phosphate (DHAP) by glycerol phosphate dehydrogenase and NAD+. DHAP can then be converted to pyruvate and then acetyl-CoA to be used in the Krebs cycle to generate ATP.
In fatty acid oxidation, what happens to the free fatty acids?
They are activated with coenzyme A to form a thioester linkage in acyl-coenzyme A. The reaction is carried out by the ligase, acyl-CoA synthetase and the energy from ATP ► AMP + PPi (pyrophosphate) ► 2Pi (orthophosphate). AMP is released. Acyl-CoA can not be used in β-oxidation.
What enzyme hydrolyzes pyrophosphate (PPi) to orthophosphate (Pi)?
pyrophosphatase
Where does β-oxidation of fatty acids occur?
mitochondrial matrix
In β-oxidation of fatty acids, what happens to the fatty acyl-coenzyme A?
It is oxidized by FAD and acyl-CoA dehydrogenase to form enoyl-CoA.
In β-oxidation of fatty acids, what happens to enoyl-coA?
It is hydrated by water and enoyl-CoA hydratase to form L-Hydroxyacyl-CoA.
In β-oxidation of fatty acids, what happens to L-Hydroxyacyl-CoA?
It is oxidized by NAD+ and L-3-hydroxyacyl-CoA dehydrogenase to form ketoacyl-CoA. NADH is released.
In β-oxidation of fatty acids, what happens to ketoacyl-CoA?
It is cleaved by β-ketothiolase which uses CoA to form acetyl-CoA and a fatty acyl-CoA (2 carbons shorter than the original). Acetyl-CoA can then be used in the Krebs cycle to generate ATP.
A fatty acid chain of 16 carbons will form how many units for oxidation? How many β-oxidation cycles will it need to go through?
It will form 8 units, in 7 cycles.
What is the issue with oxidizing unsaturated fatty acids?
Any double bonds that are in the β,γ-position must be converted to the α,β-position by isomerase in order to be used in β-oxidation.
Considering the breakdown of fatty acid chains in β-oxidation, what happens to an odd-numbered chain? For example, what about an 11-carbon chain?
It will not make as many 2-carbon units.
An 11-carbon chain will make 4 2-carbon units and 1 3-carbon unit in 4 cycles.
What is the urea cycle?
When amino acids are broken down to be used in the Krebs cycle, ammonium is released from their amino group. The urea cycle converts ammonium to urea for excretion in vertebrates.
How are amino acids converted to α-keto acids for the Krebs cycle? Where does this occur?
They are reacted with α-ketoglutarate to form an α-keto acid and glutamate, with the help of an aa-specific transaminase, aminotransferase with the coenzyme pyridoxal phosphate (PLP).
This occurs mostly in the cytosol of liver cells.
What happens to glutamate in the breakdown of amino acids?
It is oxidatively deaminated by glutamate dehydrogenase and NAD+ or NADP+ to form α-ketoglutarate, releasing NADH or NADPH and NH4+.
How do birds and reptiles deal with ammonia buildup?
They convert it to uric acid for excretion.
How do aquatic organisms deal with the buildup of ammonia?
They can excrete it as is.
What happens to ketogenic amino acids?
They are degraded to acetyl-CoA and acetoacetyl-CoA to eventually form keton bodies.
Where does the urea cycle take place?
In the mitrochondrial matrix.
After amino acids have been broken down, what happens to NH4+ in vertebrates? How does this finally release urea?
It combines with CO2 to form carbamoyl phosphate with the help of 2ATP and carbamoyl phosphate synthetase. It is then converted to citrulline ► arginosuccinate ► arginine ► ornithine. Urea is released when arginine is hydrolyzed to ornithine.
