Chapter 11 Glycolysis and Gluconeogenesis Flashcards
How does galactose enter into the glycolytic pathway?
The Leloir Pathway
What are the main steps of the Leloir Pathway?
Galactose to Galactose 1- phosphate (reaction catalyzed by galactokinase)
Galactose 1- phosphate to UDP-Galactose catalyzed by uridylyl transferase. In this step we also get Glucose 1-phosphate which is converted to Glucose 6-phosphate (reaction catalyzed by phosphoglucomutase) KEY REACTION FOR ENTERING GLYCOLYSIS!!
UDP-Galactose is oxidized to the carbonyl by UDP Glucose 4-epimerase.
NADH reduces the C-4 carbon, this generates UDP-Glucose.
Explain the significance of the Leloir pathway?
The significance of the Leloir Pathway is it gives a way for lactose to be converted to galactose. This galactose can be converted to UDP-glucose and in the process Glucose-1-phosphate is converted to Glucose-6-phosphate which is a key metabolic intermediate for glycolysis.
What is the first step of glycolysis?
Glucose is converted to Glucose-6-phosphate by hexokinase.
What is the importance of converting Glucose to Glucose-6-phosphate?
This allows to capture glucose-6-phosphate in the cell because there are no transporters for phosphorylated glucose and the negative charge make it impossible for passive diffusion.
What is the relationship between glucose-6-phosphate and hexokinase?
Glucose-6-phosphate is an allosteric inhibitor of hexokinase.
How is the first step of glycolysis made energetically favorable?
By coupling the reaction to the hydrolysis of ATP.
How is the induced fit property of hexokinase used to prevent unfavorable reactions from happening?
Hexokinase is active once glucose is bound, this prevents ATP from transferring a phosphate to water.
What is the second step of glycolysis?
Isomerization of glucose-6-phosphate to fructose 6-phosphate by phosphohexose isomerase.
What is the reaction mechanism of the isomerization of glucose-6-phosphate to fructose-6-phosphate?
Refer to slides, proton is abstracted from one place and put back in another place which results in isomerization.
In the first step of the phosphohexose isomerase reaction the enzyme abstracts a proton from glucose. Aliphatic protons are in general not acidic, why can the enzyme abstract this particular proton?
Electron withdrawal effects by adjacent carbonyl and nearby hydroxyl group.
Why is the isomerization of glucose-6-phosphate to fructose-6-phosphate favorable for the subsequent steps of glycolysis?
The reverse aldol in subsequent steps would give a 2 carbon molecule and a 3 carbon molecule instead of two structurally similar 3 carbon molecules.
What is the third step of glycolysis?
Reaction of fructose-6-phosphate to fructose 1,6-bisphosphate. Catalyzed by phosphofructokinase 1. THIS IS THE FIRST COMMITTED STEP OF GLYCOLYSIS.
What is the fourth step of glycolysis?
Reaction of fructose 1,6-bisphosphate to dihydroxyacetone phosphate and glyceraldehyde phosphate catalyzed by an aldolase.
What is the reaction that is taking place for fructose-1,6-bisphosphate to glyceraldehyde 3-phosphate and dihydroxyacetone phosphate
Reverse Aldol reaction
What is the fifth reaction step of glycolysis?
Dihydroxyacetone is converted to glyceraldehyde 3-phosphate by the enzyme triose phosphate isomerase.
What is the fifth reaction step of glycolysis?
Dihydroxyacetone is converted to glyceraldehyde 3-phosphate by the enzyme triose phosphate isomerase.
What is the relationship of ATP and PFK-1?
ATP is both acting as a substrate and allosteric inhibitor of PFK-1
How does triose phosphate isomerase prevent unfavorable side reactions?
with the endiol intermediate, stabilizing endiol intermediate prevents intermediate from undergoing dehydration.
Loop closes over the active site functioning like a lid that prevents the intermediate from detaching from the enzyme and participating in unfavorable side chemistry.
The TIM NUMBERS
GAP 123: 435261
What is the first energy recovering step reaction of glycolysis?
Reaction 6 the GAPDH reaction.
What is the sixth reaction of glycolysis?
Glyceraldehyde 3-phosphate to 1,3-bisphosphoglycerate.
What is the sixth reaction of glycolysis?
Glyceraldehyde 3-phosphate to 1,3-bisphosphoglycerate using the enzyme glyceraldehyde 3-phosphate dehydrogenase.
The addition of a phosphate group to a carboxylic acid to form a mixed ester is unfavorable. How does this reaction proceed in the GADPH reaction?
The reaction can be viewed as two separate steps:
1. the oxidation of glyceraldehyde to the carboxylic acid. (FAVORABLE)
- the phosphorylation of the carboxylic acid (unfavorable)
The addition of a phosphate group to a carboxylic acid to form a mixed ester is unfavorable. How does this reaction proceed in the GADPH reaction?
The reaction can be viewed as two separate steps:
1. the oxidation of glyceraldehyde to the carboxylic acid. (FAVORABLE)
- the phosphorylation of the carboxylic acid (unfavorable)
What is the role of the thiohemiacetal in the GADPH reaction?
We bring in a cysteine, form a thiohemiacetal and we oxidize the thiohemiacetal since it can undergo any resonance.
What is the leaving group of the GADPH reaction?
The protein is the leaving group, nucleophile: inorganic phosphate. Electrophile: thioester.
What is the seventh step of glycolysis?
1,3-bisphosphoglycerate to 3-phosphoglycerate by the enzyme phosphoglycerate kinase.
What is the first energy recovering step in glycolysis?
glyceraldehyde 3-phosphate to 1,3-bisphosphoglycerate
What is the meaning of the term substrate level phosphorylation?
phosphate group is transferred from a substrate molecule directly to ADP forming ATP.
Why do we say that phosphoglycerate kinase participates in super-coupling?
there is coupling between two distinct steps to drive the reaction forward.
1. using free energy of hydrolysis of 1,3-bisphosphoglycerate to drive synthesis of ATP.
- 1,3-bisphosphoglycerate was synthesized using free energy of oxidation of glyceraldehyde 3-phosphate.
How is glycolysis directly linked to oxygen transport?
2,3-BPG is a molecule that is produced as an intermediate in the glycolytic pathway from 1,3-bisphosphoglycerate.
What enzyme catalyzes the critical connection between 1,3-BPG and 2,3-BPG?
bisphosphoglycerate mutase.
What is the role of 2,3-BPG?
binds to hemoglobin in red blood cells and reduces its affinity for oxygen.
What is the 8th step of glycolysis?
3-phosphoglycerate to 2-phosphoglycerate by the enzyme phosphoglycerate mutase.
What is the unusual chemical bond that is present in the mutase mechanism?
the direct nitrogen to phosphorous bond.
Is the phosphate group moved directly between the oxygens on carbon-2 and on carbon-3?
No the OH on carbon two picks up phosphate from the direct nitrogen to phosphorous bond in the enzyme. The reaction goes through 2,3-BPG intermediate. The phosphate on carbon 3 is taken by the enzyme.
Pre-existing phosphate group in enzyme attached to histidine is used.
What is the 9th step of glycolysis?
2-phosphoglycerate to phosphoenolpyruvate by the enzyme enolase.
Which mechanism uses three distinct types of catalysis?
the enolase mechanism in ninth step of glycolysis:
1. acid base catalysis
2. metal ion catalysis
3. isomerization catalysis
What is the 10th step of glycolysis?
phosphoenolpyruvate to pyruvate by enzyme pyruvate kinase.
What is the second substrate level phosphorylation in glycolysis?
phosphoenolpyruvate to pyruvate by enzyme pyruvate kinase.
Which reactions of glycolysis have large negative free energies?
- glucose to glucose-6-phosphate
- fructose-6-phosphate to fructose-1,6-bisphosphate
- phosphoenolpyruvate to pyruvate
These are the regulated steps because they are committed steps that drive the reaction forward.
What are the two fates of pyruvate?
Anaerobic: fermentation takes pyruvate to other small molecule metabolites such as ethanol or lactate.
Aerobic: pyruvate is routed into the citric acid cycle.
What is the purpose of the fermentation steps in anaerobic organisms?
Get rid of NADH, so that we have continual supply of NAD+ to undergo glycolysis.
What does lactic acid fermentation involve?
Putting the electrons of NADH onto pyruvate to generate L-Lactate using enzyme lactate dehydrogenase.
What does ethanol fermentation involve?
pyruvate to acetaldehye using cofactor TPP and enzyme pyruvate decarboxylase . Then acetaldehyde is converted to ethanol by enzyme alcohol dehydrogenase.
What is the role of the TPP cofactor in ethanol fermentation?
acts as a temporary place to store the electrons from the loss of CO2.
Draw the chemical mechanism of pyruvate carboxylase.
What are the two major regulatory points for glycolysis?
pyruvate kinase and phosphofructokinase-1.
How is pyruvate kinase regulated?
The pyruvate kinase in glycolytic tissues are positively allosterically regulated by Fructose-1,6-bisphosphate. Negatively allosterically regulated by ATP, acetyl coA, and alanine
The pyruvate kinase in liver becomes inactivated when phosphorylated by protein kinase A (G alpha stimulatory pathway) and active when dephosphorylated.
How is phosphofructokinase-1 (PFK-1) regulated?
PFK-1 is positively regulated by ADP and AMP. PFK-1 is negatively regulated by ATP and citrate.
Fructose 2,6-bisphosphate positively regulates PFK-1 which stimulated glycolysis and inhibits gluconeogenesis.
What is PFK-2 (phosphofructokinase-2)?
converts fructose-6-phosphate to fructose-2,6-bisphosphate.
What is FBPase-2?
converts fructose-2,6-bisphosphate to fructose-6-phosphate.
What is importance of PFK-2?
PFK-2 synthesizes some of fructose to fructose-2,6-bisphosphate in order to regulate glycolysis.
What is a substrate cycle?
when two overlapping pathways run in opposite directions, have some enzymes in common while others differ.
Why are bypass reactions necessary in gluconeogenesis?
complimentary reactions in glycolysis are extremely exergonic.
In the first bypass reaction of gluconeogenesis how is the bicarbonate activated?
The bicarbonate is phosphorylated.
Explain the mechanism of the first bypass reaction of gluconeogenesis
refer to slides
Why was CO2 attached to pyruvate to make oxaloacetate only for it to be liberated one step later?
The CO2 was jammed onto pyruvate and taken off to provide energy because the chemistry for putting on the CO2 and taking off the CO2 are completely different.
Why when starting gluconeogenesis from pyruvate is oxaloacetate exported from the mitochondria in the form of malate?
There is no transporter for oxaloacetate out of the mitochondria. Oxaloacetate transported from the mitochondria in the form of malate through the malate shuttle.
Oxaloacetate exported from the mitochondria in the form of malate, how is this necessary and advantageous?
Electrons in NADH go on malate
We net moved out net reducing equivalents of NADH from mitochondria to cytosol (where it is rare) in the right amount.
Why does final bypass reaction take place in ER?
Glycolysis takes place in cytoplasm, this prevents glucose-6-phosphate being generated in glycolysis from being stripped off of its phosphate.
What is the major regulatory step of glycolysis and gluconeogenesis?
The PFK-1/FBPase-1 step
What is the special structural property of PFK-2 and FBPase-2?
They are both part of a single protein that has two active sites.
Explain the regulation of PFK-2/FBPase-2?
Single phosphorylation event regulates which enzyme is on or off.
High glucose—> insulin activates another phosphatase which takes off phosphate from PFK-2/FBPase-2
PFK-2 turns on, FBPase-2 turns off.
(GLYCOLYSIS ACTIVATED, INHIBIT GLUCONEOGENESIS).
Low glucose —-> release of glucagon—> activates cAMP dependent protein (protein kinase A) —-> kinase phosphorylates PFK-2/FBPase-2.
PFK-2 turns off, FBPase-2 turns on.
(INHIBIT GLYCOLYSIS, ACTIVATE GLUCONEOGENESIS)
What is the Cori cycle?
metabolic pathway that occurs between the liver and skeletal muscle.
Allows for recycling of lactate in skeletal muscle back into glucose in the liver.
What is the Forkhead box other transcription factor (FOXO1)?
stimulates the synthesis of genes for gluconeogenesis and suppresses glycolytic genes. It carries out these functions in the unphosphorylated state.
How can FOXO1 be phosphorylated?
By protein kinase B through the insulin signaling pathway.
Phosphorylated FOXO1 is a substrate for…
ubiquitination enzymes
What does glucagon do to FOXO1?
Inhibits phosphorylation of FOXO1 allowing it to continue as a transcriptional regulator.
How do insulin and glucagon regulate the expression of PEPCK?
Insulin downregulates PEPCK through insulin signaling.
Glucagon upregulates PEPCK through cAMP signaling.
Why does excess gluconeogenesis occur in type II diabetes?
Diabetes is not responding to insulin signaling pathway and is therefore not downregulating gluconeogenesis.
Why is it probably not a good idea to overexpress PEPCK in your muscles in an attempt to develop superhuman powers?
We will become extremely aggressive, uncontrolled aggression.
Explain the complete mechanism by which glucose regulates the release of insulin present in a diabetic patient.
Glucokinase present at high glucose concentrations.
Glucose enters the pancreas and
is converted to Glucose-6-phosphate.
Glucose-6-Phosphate leads to the
production of ATP through a specific pathway.
ATP causes potassium ions to stay in the cell. Calcium ions enter cell.
The increase in calcium leads to the release of insulin.
