molecular processes Flashcards
Summarise the five main functions of the Krebs cycle.
- metabolic engine
- oxidation of Acetyl-coA
- CO₂ emission
- reducing equivalent production (i.e. NADH and FADH₂)
- GTP production
(approx. 10 ATP/cycle produced)
State the reducing equivalents and how they react in the Krebs cycle.
- NAD⁺ reduction as it loses a hydride (H-) ion and a proton (H⁺): NAD⁺ → NADH + H⁺
- FAD⁺ undergoes sequential reduction by hydrogen addition: FAD⁺ + H⁺ → FADH + H⁺ → FADH₂
Describe how enzymes of the Krebs cycle are named.
- oxidoreductase → oxidation reactions to produce NADH and FADH₂
- dehydrogenases → reactions involve loss of hydrogen (H)
Describe reaction 1 of the Krebs cycle.
Hint - Owen and Chris 2- the enzyme synthesizes this product
- favourable under standard conditions
- reaction driven by formation of citryl-coA intermediate which undergoes rapid hydrolysis
- oxaloacetate + acetyl CoA → citrate (citrate synthase)
- alongside: H₂O → CoA
(draw out using notes)
Describe reaction 2 of the Krebs cycle (2-step isomerisation).
(Hint - Can’t Carry It 2)
- step 1: citrate -H₂O → cis-acotinate/intermediate (aconintase)
- step 2: cis-acotinate/intermediate +H₂O → isocitrate (aconintase)
- coordination of OH group in step 1
- facilitation of rehydration in step 2 by active site 4Fe-4S cluster
- mitochondrial form of aconitase enzyme used
Describe reaction 3 of the Krebs cycle (2-step decarboxylation and formation of NADH).
(Hint - India Owns A 3)
- step 1: oxidation:
isocitrate → (isocitrate dehydrogenase) oxalosuccinate intermediate - Step 2: decarboxylation
oxalosuccinate intermediate → (isocitrate dehydrogenase) α-ketoglutarate - isocitrate dehydrogenase tightly-regulated
- metabolic nodal point – other pathways produce α-ketoglutarate
Describe reaction 4 of the Krebs cycle (oxidative decarboxylation with NADH formation)
(Hint - Andy 1-2-3 Splat 4)
- enzymatic mechanism with 3 subunits which catalyse different stages of reaction
- α-ketoglutarate → [E1 +TPP (+ ↪CO₂) → E2 + lipoamide (+ ↪CoA) → E3 + FAD⁺ (+ ↪ NAD⁺ → NADH + H⁺)] aka the α-ketoglutarate dehydrogenase complex (intermediate) → succinyl CoA
- note 1. is decarboxylation and 3. is oxidation of lipoamide
(see notes for details)
Describe reaction 5 of the Krebs cycle (substrate-phosphorylation).
(Hint - Sally Surfs 5)
- succinyl-CoA → Succinate (succinyl-CoA synthase)
- alongside: GDP + ADP → (nuceloside diphosphate kinase) GTP + ATP
- enters E.T.C
(phosphoryl transfer)
Describe reaction 6 of the Krebs cycle (reduction)
Hint - Sianise Flies 6
- succinate → (succinate dehydrogenase) fumarate
- alongside reduction: FAD → FADH₂
- FADH₂ enters E.T.C via reduction of coenzyme Q10 in inner membrane of mitochondria
- succinate dehydrogenase associated with membrane, and covalently-linked to FADH₂ molecule
Describe reaction 7 of the Krebs cycle (hydration)
Hint - Freya Can’t Match 7
- fumarate → (fumarase + OH-) carboanion intermediate (fumarase + H⁺) → malate
- hydration of C=C catalysed by stereospecific enzyme
- formation of L-isomer of malate which is important for metabolite transporters across mitochondrial membranes
Describe reaction 8 of the Krebs cycle (oxidation)
Hint - Marley Owns 8
- malate → oxaloacetate (malate dehydrogenase)
- alongside: NAD⁺ → NADH + H⁺ (reduction)
- oxidation of OH group regenerates oxaloacetate
How is the Krebs/Citric acid cycle studied and what happens to the carbons from acetyl CoA and how are some carbons lost?
- carbons from Acetyl-coA are not ones lost via decarboxylation reactions
- acetyl-coA carbons become incorporated into oxaloacetate at the end of the cycle
- thus lost as CO₂ in subsequent turns of cycle
- explored using 14C-labelling experiments
(see notes for summary drawing of cycle)
What drives the Krebs cycle?
Hint - to do with ΔG and certain steps
- ΔG difficult to determine as in mitochondria and isolating w/o contaminating with cytosol difficult
- steps 1, 3 and 4 → key regulatory points
- step 8 not spontaneous with low oxaloacetate concentrations → can drive reaction forward
Name five enzymes which are key in regulating the Krebs cycle.
(Hint - PICAP - 1x creation, 3x remove H, remove CO₂ - α)
- citrate synthase
- isocitrate dehydrogenase
- α-ketoglutarate dehydrogenase
- pyruvate dehydrogenase
- pyruvate decarboxylase
Describe oxidative phosphorylation in mitochondria.
- 4 enzymes complexes (lots of proteins in them) embedded in membrane
- NADH as e- donor passes through complex 1 (ubiquinone/nol) and 4 H⁺ pass through
- with FADH₂ less ⁺ pumped → less ATP synthesis
• QH is shuttle molecule
• terminal complex so oxygen reduced to water
(see notes for diagrams)
What is reduction potential and what does it mean?
- tendency of a species to accept electrons/become reduced
- more positive the value the more likely to accept electrons
- relative to a proton
- biochemical standard reduction potential (E°’) is for a compound under standard conditions (like G°’)
- as you go along ETC reduction potential of substrates increases
- O₂ + 2H⁺ + 2e- → H₂O
What is the general formula of saturated fatty acids?
- CH₃(CH₂)nCOOH
- contain HC chain, terminal carboxylic acid group and cis or trans bonds
Give 4 examples of saturated fatty acids.
- stearic acid; octadecanoic acid, 1st C=C at C1, 18 Cs
- oleic acid; ω 9-fatty acid, 1st C=C at C9, 18 Cs
- linoleic acid; ω 6-fatty acid, 1st C=C at C6, 18 Cs
- α-linoleic acid; ω 3-fatty acid 1st C=C at C3, 10 Cs
(see notes for details)
Describe triacylglycerol metabolism.
- glucose can be converted into fatty acyl glycerol
- hormone-sensitive lipase used to conjugate fats to lipids and then transport fats
- intracellular (unlike from lipoprotein + pancreatic lipase)
- TAG → DAG → MAG → FFA + glycerol
TAG = triacyl glycerol DAG = diacyl glycerol MAG = monoacyl glycerol FFA = free fatty acid
What do high glucose levels cause for hormone-sensitive lipase?
- inhibition of lipolysis (fat breakdown)
- provides glycerol-3-phosphate from glycolysis
- thus, promotes fat storage
What are the 4 main roles of fatty acids?
Hint - Faisah Served Colourful Halvah
- fuel molecules – mostly stored in adipose tissue as triacylglycerols (i.e. triacylglycerol metabolism)
- structural – component of lipid membranes as attached to groups
- covalent modifications of proteins (dynamic and reversible)
- increase interaction w/ membranes (lipid anchors)
- promote protein-protein interactions - production of fatty acid hormones - i.e. prostaglandins stimulate inflammation, modulate synaptic transmission, stimulate sleep
Why is fatty acid synthesis regulated?
- so catabolism (mitochondria) and anabolism (cytoplasm) don’t simultaneously occur (pathways not simply reversals of one another)
What is stage 1 of fatty acid synthesis?
Hint - AM and lots of other molecules involved
- acetyl CoA → (acetyl CoA carboxylase, ACC) malonyl CoA
- alongside: HCO₃- + ATP → ADP + Pi
- first step, irreversible, rate-limiting, allosteric enzyme
- requires biotin (vitamin B7) and ATP
(see notes for details)
What is stage 2 of fatty acid synthesis?
Hint - CoACP
1) acetyl CoA → acetyl ACP (acetyl trancylase)
- alongside: ACP → CoA
2) malonyl CoA → malonylACp (malonyl transacylase)
- alongside: (another) ACP → CoA
- ACP is a transport protein which binds to acetyl