Metabolism 4 Flashcards
Semester 1 year 1
What happens in the Link reaction?
-pyruvate oxidised to acetyl CoA + CO2
-in anaerobic conditions
-1 molecule of NADH formed
What enzymes are in the pyruvate dehydrogenase complex?
-pyruvate decarboxylase
-dihydrolipoyl transacetylase - transfers acetyl fragment
-dihydrolipoyl dehydrogenase - transfers electrons to NADH
What cofactors do pyruvate dehydrogenase bind to?
-thiamine pyrophosphate (TPP)
-lipoamide
-FAD/FADH2
-coenzyme A
-NAD+/NADH
Describe coenzyme A
-an activated carrier molecule - carries acetyl group via thioester linkage
-hydrolysis of linkage in energetically favourable
-can be coupled with a +ΔG reaction
What is FAD and how is it different from NAD+?
-FAD = activated carrier molecule that can carry 2 e- (like NADH)
-binds 2 protons rather than 1 when reduced, becoming FADH2
Describe step 1 of the Link reaction
-pyruvate is decarboxylated to CO2 + hydroxy-ethyl fragment
-carried out by pyruvate dehydrogenase
-the fragment is bound to a TPP cofactor on pyruvate decarboxylase
-loss of carboxyl group (+3) as CO2 (+4) provides an electron for C2 carbon to become C-
Describe step 2 of the Link reaction
-hydroxy-ethyl-TPP oxidised to ethyl fragment by lipoamide cofactor on dihydrolipoyl transacetylase
-forms acetyl-dihydrolipoamide
Describe step 3 of the Link reaction
-acetyl-dihydrolipoamide reacts with coenzyme A to form acetyl CoA + dihydrolipoamide
-these are oxidised by FAD cofactor to form FADH2
-FADH2 reduces NAD+ to NADH
What is made in the Krebs cycle?
-lots of electron carriers
-makes ATP by substrate level phosphorylation
What are the steps of the Krebs cycle?
- citrate formation
- citrate isomerisation
- the first decarboxylation
- the second decarboxylation
- ATP formation
- succinate oxidation
- fumarate hydration
- malate oxidation
Describe the first step of the Krebs cycle
-citrate synthase removes proton from methyl group on acetyl CoA to form CH2^-
-CH2^- acts as a nucleophile towards carbonyl group of oxaloacetate
-energetically favourable CoA-intermediate hydrolysis drives the forward reaction
Describe the second step of the Krebs cycle
-aconitase isomerises citrate (tertiary alcohol) to isocitrate (secondary alcohol)
-does this by removing water then adding it back - hydroxyl group moves from C3 to C4
-makes next reaction easier as now breaking C-H rather than C-C
Describe the third step of the Krebs cycle
-isocitrate dehydrogenase catalyses oxidation of C4
-hydroxyl group converted to carbonyl
-NAD+ molecule reduced in this process
-unstable intermediate is formed that is rapidly decarboxylated
-produces 𝛼-ketoglutarate + CO2
What is the importance of CO2?
-very stable - more so than the reactants
-easily escapes from site of reaction
-more products than reactants = +ive entropy
Describe the fourth step of the Krebs cycle
-𝛼-ketoglutarate dehydrogenase catalyses oxidation of C5 from +3 to +4 and C4 from +2 to +3
-releases CO2
-oxidation (-ΔG) coupled to NADH + succinyl CoA formation (+ΔG)
Describe the fifth step of the Krebs cycle
-succinyl-CoA synthetase catalyses hydrolysis of thioester bond
-replaced with a phosphoester bond to form succinyl phosphate
-thioester bond hydrolysis is energetically favourable
-phosphate transferred to ADP to form ATP by substrate level phosphorylation
Describe the mechanism of succinyl-CoA synthetase
-coenzyme A displaced by bound phosphate group to form succinyl phosphate
-histidine side-chain removes Pi to form succinate + phosphohistidine
-Pi group transferred to ADP forming ATP by substrate level phosphorylation
Describe the sixth step of the Krebs cycle
-succinate dehydrogenase uses FAD cofactor to oxidise succinate to fumarate
-FAD is the cofactor reduced rather than NAD+
-free energy change of the reaction is insufficient to reduce NAD+ as C=C is weaker than C=O
What is succinate dehydrogenase?
A transmembrane protein bound to inner mitochondrial membrane
Describe the seventh step of the Krebs cycle
-fumarase converts fumarate to malate by adding water across the C=C bond to form a hydroxyl group
-facilitates oxidation in step 8 by avoiding necessity for C=C formation
Describe the eighth step of the Krebs cycle
-malate dehydrogenase uses NAD+ to convert malate to oxaloacetate
-malate hydroxyl group converted to carbonyl using 2H from water to form NADH
In the Krebs cycle, what provides the oxygen for CO2?
H2O, not O2
What does it mean to say the Krebs cycle is an amphibolic cycle?
It acts catabolically and anabolically
How many NADH and FADH2 molecules are generated per acetyl CoA and per glucose?
-NADH = 3 per acetyl CoA, 6 per glucose
-FADH2 = 1 per acetyl CoA, 2 per glucose
