Metabolism 2 + 3 Flashcards
Semester 1 year 1
What happens to part of the energy released during oxidation reactions?
-coupled to generation of activated carrier molecules
-molecules then drive endergonic reactions
At equilibrium, why is there a higher concentration of ADP and Pi?
-negative charges on phosphates repel
-entropy increases
-water stabilises the product - more interactions with ADP + Pi
-free Pi stabilised by resonance structures not possible when bound to ATP
How do you calculate ΔG?
ΔG = RT ln(mass action ratio/K)
What is the mass action ratio?
The actual concentration ratio of products to reactants under a particular condition
For a dead cell, what is the ΔG for when the mass action ratio is less than, equal to or greater than K?
-< K, ΔG = -ive
-=K, ΔG = 0
->K, ΔG = +ive
In a living cell, is the mass action ratio less than, equal to or greater than K?
< K , ΔG = -ive
What defines the capacity of a reaction to do work?
The extent to which the actual concentration ratio of products to reactants (mass action ratio) is displaced from equilibrium
What are features of cofactors?
-kinetically stable - enzymes can control flow of free energy + reducing power
-thermodynamically stable
-all react slowly with O2/H2O in absence of enzyme catalyst
What is coupled in anabolic pathways and some steps in catabolism?
-endergonic reactions (+ΔG) to exergonic reactions (-ΔG)
-net -ΔG
Where does glycolysis take place?
Cytoplasm
What is the net gain of ATP and NADH in glycolysis?
Net gain of 2 ATP + 2 NADH
What are the steps of glycolysis?
- glucose phosphorylation
- isomerisation to fructose
- second phosphorylation
- cleavage
- conversion of DHAP
- oxidation of GAP
- first phosphate transfer to ADP
- isomerisation to 2-phosphoglycerate
- removal of water
- second phosphate transfer
Which steps in glycolysis are repeated?
-steps 6-10 occur twice
-each glucose molecule produces 2 pyruvate
Describe the first step of glycolysis
-2 ATP hydrolysed to release energy
-terminal phosphate transferred from ATP to 6th carbon on glucose to form G6P using enzyme hexokinase
–ive charge on Pi group means G6P trapped in cell
-keeps glucose conc. in cell low so increased glucose uptake
Describe hexokinase
-glucose binding causes conformational change
-favours direct transfer of Pi from ATP to glucose + prevents ATP hydrolysis
-active site contains aspartate - deprotonates C6 hydroxyl group on glucose
-deprotonated O- acts as nucleophile + attacks gamma Pi group of ATP
-Pi transferred directly to glucose without hydrolysis by water
Which reactions are coupled in glycolysis?
-ATP hydrolysis with addition of Pi to glucose
-results in net -ΔG
equilibrium ratio of [Glu]/[G6P] changed by factor of 10^5
Describe the second step of glycolysis
-G6P isomerised by phosphoglucose isomerase to fructose-6-phosphate (F6P)
-forms a ketose sugar from an aldose sugar - needed for step 4
-reaction readily reversible under cellular conditions
Describe the third step of glycolysis
-F6P phosphorylated by phosphofructokinase to fructose-1,6-bisphosphate (F1,6P) using ATP
-Pi group further destabilises sugar - promotes cleavage in step 4
-entry of sugars into glycolysis controlled via allosteric regulation of phosphofructokinase
Describe step 4 of glycolysis
-F1,6P is cleaved by aldolase, producing 2 3C sugars, DHAP + GAP
-DHAP converted to GAP as only GAP proceeds through glycolysis
Why is the isomerisation to fructose in step 2 important?
-ensures a 3:3 split rather than a 2:4 split
-that would require 2 separate pathways
Describe step 5 of glycolysis
-DHAP converted to a second GAP molecule by triose phosphate isomerase (TIM)
-TIM is a kinetically perfect enzyme
-TIM suppresses formation of toxic intermediate methyl glyoxal from the enediol intermediate
-does this by movement of 10 AA loop region over active site that blocks exit of enediol until GAP formed
Describe step 6 of glycolysis
-glyceraldehyde 3-phosphate dehydrogenase (GAPDH) uses NAD+ to oxidise GAP to form NADH
-enzyme couples oxidation to transfer of Pi group to the sugar to form 1,3BPG (has high phosphoryl transfer potential)
-the first energy generating step of glycolysis
How is NADH made and what is it used to make?
-energy released from carbon oxidation used to form NADH via transfer of a H- to NAD+
-used by electron transfer chain in mitochondria to make ATP by oxidative phosphorylation
Describe step 7 of glycolysis
-Pi group transferred from 1,3BPG to ADP by phosphoglycerate kinase - forms ATP + 3-phosphoglycerate (3PG)
-substrate level phosphorylation - Pi transferred from phosphosugar e.g 13BPG to ADP
-second energy generating step
-standard ΔG is -ive
-Mg2+ in active site activates ADP for reaction
Describe step 8 of glycolysis
-remaining phosphoester linkage transferred by phosphoglycerate mutase from C3 to C2
-forms 2-phosphoglycerate
-facilitates removal of water in step 9
Describe step 9 of glycolysis
-water removed from 2-phosphoglycerate by enolase, creating a molecule of phosphoenolpyruvate
-2 phosphoglycerate + PEP contain same amount of metabolic energy
-enolase reaction rearranges substrate into a form from which more of this potential energy can be released upon phosphoryl transfer
Describe step 10 of glycolysis
-transfer of phosphate group from step 9 by pyruvate kinase to ADP forms ATP + pyruvate
-the 3rd energy generating step + another substrate level phosphorylation
-reaction runs far from equilibrium + essentially irreversible
-pyruvate conc. kept low by product removal
When does fermentation occur?
-in the absence of O2
-further pyruvate oxidation can’t occur
What accumulates when O2 is absent, why and why is this bad?
-NADH
-inhibition of electron transport
-NAD+ shortage caused + glycolysis inhibited
How is the NAD+ shortage prevented when O2 is absent?
-NADH used to reduce pyruvate to lactate or ethanol
-NAD+ regenerated to restore redox balance
-ATP production continues
