2. Glycolysis Flashcards
During this process one molecule of __________ (6 carbon molecule) is degraded into two molecules of __________ (three carbon molecule).
glucose
Free energy released in this process is stored as ____ molecules of __________, and ____ molecules of __________.
2 ATP
Provide the 2 chemical equations of glycolysis, indicating which one has a negative and positive free energy change:
Glucose + 2NAD+ = 2Pyruvate + 2NADH + 2H+ (negative free E)
In standard condition glycolysis is an exergonic reaction which tends to be irreversible because of negative dGo. True or false?
TRUE
____% of total free energy that can be released by glucose is released in glycolysis.
5.2
What are the 3 different fates of glucose?
- STORAGE –> glycogen, starch, sucrose
Pasteur’s effect
Aerobic growth requires less glucose than anaerobic condition. (more consumption of sugar in anaerobic)
What did Buchner discover?
Reactions of glycolysis can be carried out in cell-free yeast extract.
What did Harden and Young discover? (2)
1: inorganic phosphate is required for fermentation.
What were the 2 major inhibitor studies of glycolysis?
Iodoacetate treatment resulted in the accumulation of fructose 1,6biphosphate.
Get info from slide 6 on importance of phosphorylated intermediates
Okay
Importance of phosphorylated intermediates: (3)
1.Possession of NEGATIVE CHARGE which inhibit their diffusion through membrane.
What is the preparatory phase of glycolysis?
Phosphorylation of glucose and its conversion to glyceraldehyde 3-phosphate (Rxns 1-5)
What is the payoff phase of glycolysis?
Oxidative conversion of glyceraldehyde 3-phosphate to pyruvate and the coupled formation of ATP and NADH
Provide the names of all glycolysis structures in order with the respective inputs and outputs and draw their structures
Looking back, I am ashamed of this question.
What are the 2 extremely important things that take place in reaction 6?
Oxidation from aldehyde to carboxylate yielding NADH and phosphorylation via inorganic phosphate
This inorganic phosphate drives the formation of net ATP. true or false?
TRUE
Also, name the substrates involved and inhibitors.
Hexokinase reaction: phosphorylation of glucose by hexokinase
This enzyme undergoes large conformational change upon binding with Glucose. True or false?
TRUE
In the liver, ____________ is the main hexokinase which prefers glucose as substrate
glucokinase
Why are un-complexed ATP and G6P very fitting as inhibitors?
Because if a lot of ATP is around, we don’t need more glycolysis and if a lot of G6P is around then we don’t need to do the first step much anymore
Name and describe the 2nd reaction of glycolysis, including what the enzyme requires for its activity:
Phosphohexose isomerase (or phosphoglucose isomerase) –> isomerization of G6P to F6P
Provide rough free energy value and explain why this rxn is favoured:
near zero but gets favoured because concentration of product is really low as a result of a highly exergonic 3rd step, so reaction is driven forward.
Also include free energy sign.
Phosphofructokinase-1 reaction: irreversible transfer of phosphoryl group from ATP to C-1 of F6P to produce F-1,6-P
Describe phosphofructokinase-1 regulation:
ATP (allosteric) and citrate are inhibitors
Also, name and describe its free energy situation:
Aldolase Reaction: Cleavage of Fructose 1,6 bisphosphate into glyceraldehyde 3 phosphate (an aldose) and dihydroxyacetone phosphate (a ketose).
Describe what aldolase does mechanistically:
cleaves f16bisphosphate by aldol condensation mechanism
Name and describe the 5th of glycolysis:
Triose phosphate isomerase: Conversion of Dihydroxyacetone phosphate to glyceraldehyde 3 Phosphate.
It is endergonic/exergonic.
reversible
Name and briefly describe what happens in 6th reaction:
Glyceraldehyde-3-phosphate dehydrogenase reaction (GAPDH): Conversion of GAP to 1,3-Bisphosphoglycerate
Remember harden and young found out that if u get rid of ___________ phosphate, reaction 6 doesn’t happen meaning glycolysis will stop
phosphoanhydride
NAD+ is a ___________, BUT ALSO acts as ___________ , taking away hydrogen
co-factor
What is the oxidizing agent in step 6?
NAD+
Evidence for the GAPDH reaction mechanism:
I.Iodoacetate inhibits this reaction, indicating the involvement of Cystine residue of enzyme.
List the steps to the reaction 6 mechanism and draw it:
1.Glyceraldehyde 3 phosphate (GAP) binding to the enzyme.
Also indicate how the enzyme catalyzes the reaction.
Phosphoglycerate Kinase Reaction: Transfer of phosphoryl group fron 1,3 bisphosphoglycerate to ADP generating ATP.
Indicate the free energy situation in reaction 7.
6th step and 7th step are coupled to generate the ATP from energy released by oxidation of GAP. 6th step is endergonic, 7th is exergonic.
The name for the 7th reaction indicates the enzymatic function for the reverse reaction. True or false?
TRUE
This step generates ATP by _____________-_____________ _____________.
substrate level phosphorylation
Name and briefly describe the 8th reaction of glycolysis.
Phosphoglycerate Mutase Reaction: Conversion of 3-phosphoglycerate to 2-phosphoglycerate (2-PG).
Provide the steps for the mechanism of reaction 8 and draw it out:
- 3-PG binds to phosphoglycerate mutase active site.
In most cells 2,3BPG is present in trace amount, but in _____________ it is present in significant amount. There it regulates _____________ affinity to _____________ .
erythrocytes
Also, indicate the free energy situation.
Enolase Reaction: Dehydration of 2-phosphoglycerate (2-PG) to phosphoenolpyruvate (PEP).
Describe the mechanism for step 9 and draw it:
- Binding of 2-PG to active site of enolase
Name and briefly describe the 10th reaction of glycolysis:
Pyruvate kinase reaction: transfer of phosphoryl group from PEP to ADP generating ATP and Pyruvate. (Sub-level phosphorylation)
What does the 10th reaction require?
Mg2+ and K+
Name is for the reverse reaction again. True or false?
TRUE
Why is the 10th reaction so favoured?
Pyruvate is resonance stabilized and can tautomerize!
Draw the 2 forms of pyruvate:
Slide 25
After balancing, provide chemical equation for glycolysis:
1Gl + 2NAD++ 2ADP + 2Pi = 2pyruvate+2ATP + 2NADH
The ___ NADH molecules are oxidized in mitochondria under aerobic condition and the free energy released is enough to synthesize ____ molecules of ATP by oxidative phosphorylation
2
Under the aerobic condition, pyruvate is catabolized further in mitochondria through ______________ ______________ and ______________ ______________ ______________ where all the carbon atoms are oxidized to ______________ . The free energy released is used in the synthesis of ATP, NADH and FADH2.
pyruvate dehydrogenase
Pyruvate is converted to __________ in __________ fermentation in ___________ or to __________ in __________ fermentation in ___________
lactate; homolactic; mammals (and some microorganisms)
1 Glucose = ____ pyruvate = ____ lactate
2
1 Glucose = ___ pyruvate = ____ ethanol + ___ co2
2
How do you make acetylcoa
2 pyruvate = 2co2 + 2acetyl coA
2 Acetyl CoA = ___co2 + ___h2o
4
Describe why homolactic fermentation is needed, what happens and where? What is the ultimate result?
Homolactic fermentation is needed in anaerobic conditions or in a sudden need of a lot of ATP. NAD+ needs to be regenerated in order to run the GAPDH reaction in which NAD+ is the oxidizing agent.
Provide a full representation of homolactic fermentation (structures, names, enzymes, reactants, products, free energy)
Slide 28
true or false?
TRUE
Describe why alcohol fermentation is needed and what happens. What enzymes are involved?
Regenerate NAD+
Indicate what each enzyme does in alcoholic fermentation and what they require to do so. (TWO steps)
1.Pyruvate decarboxylase (PDC) reaction: This enzyme is Mg++-dependent and requires an enzyme-bound cofactor, thiamine pyrophosphate (TPP). In this reaction a molecule of CO2 is released producing acetaldehyde.
What is seen in anaerobic processes compared to aerobic?
pasteur effect - more sugar consumption
Draw the functional group of thiamine pyrophosphate (TPP) involved in the mechanism (thiazolium ring):
slide 31
Describe the reaction mechanism of pyruvate decarboxylase and draw it out:
- Hydrogen comes off TPP to form a TPP anion that does a nucleophilic attack on carbonyl carbon of pyruvate.
Describe the alcohol dehydrogenase mechanism and draw it out:
- Hydride ion from NADH attacks carbonyl carbon of acetaldehyde
Two types controls for metabolic reactions and when they occur:
Substrate limited : When concentrations of reactant and products in the cell are NEAR EQUILIBRIUM, then it is the availability of substrate which decides the rate of reaction
Which reactions are the ones which control the flux of the overall pathway.
Enzyme-limited controlled reactions.
There are three steps in glycolysis that have enzymes which regulate the flux of glycolysis:
I.The hexokinase (HK)
Most important enzyme regulating flux of glycolysis is ________
PFK-1
Regulation of PFK-1:
- Inhibitors –> ATP and citrate
How does adenylate kinase work to regulate PFK?
It converts 2 ADP molecules to ATP and AMP. in Jǐnjí qíngkuàng, we need a lot of ATP so get that by converting ADP to ATP and AMP, so that AMP can inhibit phosphatase and activate PFK-1.
Does ATP slow down PFK-1 activity or block it?
slows it down!
What is the substrate cycle/futile cycle?
In order to control the flux of glycolysis and to have better regulation, cells have FBPase which keeps degrading the product of PFK reaction (FBP) to its substrate (F-6-P). This is called substrate cycle.
Why is it considered futile?
This is a futile exercise where, cells invest an ATP to produce FBP which is hydrolysed back to F6-P by FBPase. This is a price cells pay to keep glycolysis in check.
How is it not really futile tho?
Keeps cycles in check and the regulation by AMP allows for a very fast ATP production in emergency situation. This is because AMP activates PFK-1 10 fold while it also inhibits FBPase 10 fold, meaning 100-fold activation to form more ATP in jinji qingkuang.
How is hexokinase and glucokinase regulated?
It is allosterically inhibited by its product Glucose 6 phosphate. In liver Glucokinase is inhibited by Fructose 6 Phosphate. Uncomplexed ATP acts as a competitive inhibitor of this enzyme.
How is pyruvate kinase regulated?
It is allosterically inhibited by ATP. ATP binding to the inhibitor site of pyruvate kinase decreases its ability to bring to phosphoenol pyruvate (PEP) the substrate.
Glycolysis from glycogen is actually a net 3 ATP. Why?
because it enters the pathway as G6P without having to use ATP to phosphorylate.
