Metabolism Flashcards
Explain a what a disulphide bridge is
A covalent bond between two cysteines where the SH groups are oxidised.
What do chaperones do
Can be present in protein folding, ensuring it continues along the most energetically favourable route.
Why is NAD+ a co-enzyme
It has no catalytic activity of its own and only functions after binding to an enzyme.
How is pyruvate converted into ethanol?
Converted to ethanal by pyruvate decarboxylase; converted to ethanol by alcohol dehydrogenase.
Where is GTP produced in the Krebs cycle?
Conversion of succinyl-CoA to succinate, producing CoA and requiring water. Catalysed by succinyl-CoA synthetase
What is A-SCS and where is it found?
An isoform of succinyl-CoA synthetase which catalyses the conversion of succinyl-CoA to succinate, producing ATP rather than GTP. It is found in skeletal and cardiac muscle
Where are the enzymes in the TCA cycle found?
All in the mitochondrial matrix, except succinate dehydrogenase which is found in the inner mitochondrial membrane
Define transamination
Reaction in which an amine group is transferred from one amino acid to a keto acid to form a new pair of keto and amino acids.
What molecules and enzymes are involved in the glycerol phosphate shuttle? How does the shuttle work?
DHAP (dihydroxyacetone phosphate) and glycerol-3-phopshate. Cytoplasmic and mitochondrial glycerol-3-phosphate dehydrogenase. FADH2 produced which communicates directly with ubiquinone.
What is the Warburg effect?
The preferential generation of lactate even under conditions of ample O2.
Name the 3 enzymes in the pyruvate dehydrogenase complex
Pyruvate decarboxylase
Dihydrolipoyl transacetylase
Dihydrolipoyl dehydrogenase
Describe how the pyruvate dehydrogenase complex works
- Decarboxylation of pyruvate by pyruvate decarboxylase to produce hydroxyethyl TPP.
- Oxidation and transfer to lipoamide to give acetyl-lipoamide.
- Transfer of the acetyl group to CoA.
- Regeneration of oxidised lipoamide (reactions 2-4 are all catalysed by Dihydrolipoyl transacetylase.
- Regeneration of oxidised FAD, regenerating NADH, by the enzyme Dihydrolipoyl dehydrogenase.
What is (thiamine pyrophosphate) TPP?
A derivative of vitamin B which readily loses a proton to react with pyruvate to from hydroxyethyl-TPP. Catalysed by pyruvate dehydrogenase;
Which type of processes use NADPH as a co-enzyme?
Anabolic processes
Define substrate level phosphorylation
Direct transfer of a high-energy phosphate group from an intermediate to ADP to produce ATP.
What does the proton-motive force which drives protons from the intermembrane space back into the matrix consist of?
A pH gradient AND a transmembrane electrical potential.
Name the 3 complexes and 2 mobile carriers of the ETC.
NADH dehydrogenase complex, cytochrome b-c1 complex, cytochrome oxidase complex.
Co-enzyme Q (ubiquinone) and cytochrome C.
How is it ensured electrons travel in the right direction down the ETC?
Each unit in the chain has a higher affinity for electrons than the previous unit.
How is ubiquinone confined to the inner mitochondrial membrane?
It has a hydrophobic tail
What does a negative redox potential indicates?
A tendency to donate electrons.
Why does FADH2 produce less ATP than NADH in oxidative phosphorylation?
Succinate dehydrogenase communicates directly with co-enzyme Q, so fewer protons are pumped across the inner mitochondrial membrane per electron.
How does cyanide (and azide) act as a metabolic poison?
It has a high affinity to the ferric (3+) haem group in the cytochrome oxidase complex. It’s binding blocks the flow of electrons through the ETC, stopping ATP production.
How does malonate act as a metabolic poison?
Malonate closely resembles succinate so is a competitive inhibitor for succinate dehydrogenase. By inhibiting the oxidation of succinate to fumarate, the flow of electrons is reduced.
How do aromatic weak acids, such a DNP, uncouple oxidative phosphorylation from ATP synthesis?
DNP can cross the membrane in its undissociated form: hence it accepts a proton on the intermembrane side, crosses the membrane and releases the proton into the matrix. This dissipates the proton gradient. This causes the ETC to run uncontrollably, producing lots of heat as waste energy.
Describe how the uncoupling of oxidative phosphorylation can be regulated (non-shivering thermogenesis).
UCP-1 / Thermogenin is a channel that can be activated by a drop in core body temperature. It allows protons to bypass ATP synthase, releasing heat from the dissipation of the proton gradient.
Recall B-oxidation.
Fatty acid –> acyl-CoA using 2 ATPs.
Acyl group transferred to carnitine by carnitine acyl-transferase. Acyl Carnitine crosses into the matrix using a translocase.
Fatty acyl-CoA then oxidised by acyl-CoA dehydrogenase, giving FADH2.
Hydrolyses
Oxidised to give NADH
Thiolysis using B-ketothiolase –> acetyl-CoA produced
Give the overall equation for the B-oxidation of palmitate (palmitic acid)
Palmitoyl-CoA + 7FAD + 7NAD+ + 7CoA –> 8 acetyl-CoA + 7FADH2 + 7NADH + 7H+
How do bile salts (produced in the liver and stored in the gall bladder) emulsify fats?
They have a hydrophobic face and hydrophilic face allowing the bile slats to interact with the triacylglycerols and solute.
Pancreatic lipases digest triacylglycerols emulsified by bile salts forming mixed micelles, which contain…
Triacyl-, diacyl- and monoacylglycerols, free fatty acids, bile salts, cholesterol, lysophosphatidic acid and fat soluble vitamins. Mixed micelles are taken up by enterocytes.
Why is storing food as triacylglycerols a good way of compact food storage?
Triacylglycerols are anhydrous: Glycogen needs water to be kept soluble: 2g of water per gram of glycogen.
Recall lipogenesis
Acetyl-CoA + HCO3 –> Malonyl CoA (3C) requiring ATP via acetyl CoA carboxylase
Malonyl CoA + ACP –> Malonyl ACP + CoA via Malonyl-CoA-ACP transferase
Acetyl-CoA + ACP –> Acetyl-ACP + CoA via Acetyl-CoA-ACP transferase
B-ketoacyl ACP synthase condenses Acetyl-ACP and Malonyl-ACP to produce Acetoacetyl ACP + ACP + CO2
Reduction by ketoreductase to form NADP+
Dehydration
Reduction by enol reductase to form NADP+
Elongation by further malonyl ACP condensation.
Finally hydrated to remove ACP.
Give key differences between fatty acid metabolism and synthesis
Carriers: CoA vs ACP
Reducing power: FAD/NAD+ vs NADPH
Give the overall equation for the synthesis of palmitate
Acetyl-CoA + 7Malonyl-CoA + 14NADPH + 14H+ –> palmitate + 7CO2 + 6H20 + 8 CoA + 14NADP+
Detail cholesterol biosynthesis
2 acetyl-CoA molecules combine by B-ketothiolase to form Acetoacetyl-CoA. A third acetyl-CoA combines via HMG-CoA synthase.
HMG-CoA is reduced to mevalonate, forming 2 molecules of NADP+
Mevalonate undergoes sequential phosphorylation and decarboxylation to form an activated isoprene unit.
3 of these condense to form farnesyl pyrophosphate.
2 farnesyl pyrophosphate molecules condense via squalene synthase, generating NADP+
Squalene is cyclised to cholesterol
How are steroids derived from cholesterol?
Desmolase converts cholesterol into pregnenolone, the precursor for all 5 classes of steroid hormone.
Where is lipoprotein lipase found and what does it do?
It is found in capillary endothelial cells
Hydrolyses triacylglycerols to glycerol and fatty acids
Fatty acids are then used in beta-oxidation.
Glycerol is returned to the liver for gluconeogenesis
What is the role of apoproteins in lipoproteins?
Allow the lipoprotein to be recognised by tissues as apoprotein varies between different types of lipoprotein.
How do statins reduce the accumulation of cholesterol? Give an example.
Statins are HMG-CoA Reductase inhibitors
Lovastatin – competitively inhibits HMG-CoA Reductase
What is reverse cholesterol transport?
The transport of cholesterol by HDLs from the peripheral tissues back to the liver for use or disposal.
What happens to digested dietary products after uptake by enterocytes?
TAGs are resynthesised and incorporated into chylomicrons (the least dense lipoproteins). They are transported via the lymphatic system from the thoracic duct to the left subclavian vein where they enter circulation. (Chyle).
How are nuclear proteins imported?
Import receptors on nuclear envelope recognise nuclear localisation signals attached to the protein.
Give examples of post-translational modifications in the ER lumen
Folding, formation of disulphide bridges, initial glycosylation, proteolytic cleavages.
Name the 5 compartments of the Golgi apparatus, in the order of protein movement.
Cis-Golgi network –> cis cisterna –> medial cisterna –> trans cisterna (the cisternae make up the Golgi stack) –> trans-Golgi network.
Define constitutive secretion
Unregulated exocytosis: a steady stream of vesicles from the trans Golgi network to the plasma membrane.
Define regulated secretion
The products of the Golgi are concentrated and stored in secretory vesicles until an extracellular signal stimulates their secretion.
What does dynamin do?
Forms a ring around the neck of a deeply-invaginated coated pit, pinching of the vesicle from the plasma membrane.
Describe receptor-mediated endocytosis.
Molecule binds to receptor. Formation of clathrin-coated vesicle. Uncoating. Fusion with endosome. Delivery to lysosome. Receptor buds off from endosome in transport vesicle and is returned to the plasma membrane.
Describe the structure of creatine kinase and its distribution.
It is a dimer. There are 2 monomers: a B and M monomer. The only place in the body which expresses BM is cardiac muscle.
How is CK activity in the serum detected?
A coupled assay which produces a detectable product (in this case NADPH, monitored by UV absorbance).
How is levels of CK BM isoform in the plasma directly proportional to the amount of cell death?
Each myocyte considered equal volume, so releases a ‘quantum’ of CK into extracellular fluid (and hence into the plasma).
What is the pI.
Isoelectric point: the pH at which a molecule has no overall charge.
What inhibits NADH dehydrogenase?
Rotenone.
Why is NAD+ described as a coenzyme?
It has no catalytic activity of its own and only functions after binding to an enzyme.
Describe the transamination of alanine with a-ketoglutarate.
Catalysed by alanine aminotransferase.
Pyruvate enters the Krebs cycle; glutamate is converted to a-ketoglutarate by glutamate dehydrogenase.
Where would you find the glycerol phosphate shuttle, and where would you find the malate-aspartate shuttle?
Glycerol phosphate found in skeletal muscle and the brain.
Malate aspartate found in the liver, kidney and heart.
Describe the transamination reaction in the malate-aspartate shuttle
Glutamate and oxaloacetate become a-ketoglutarate and aspartate.
How does oligomycin act as a metabolic poison?
It’s an antibiotic which binds to the stalk of ATP synthase, preventing H+ flow and causing the concentration of H+ in the intermembrane space to increase to the saturation point where no more H+ can be pumped out by the ETC.
What is medium-chain acyl-coenzyme A dehydrogenase deficiency (MCADD) detected by and responsible for?
Detected by HEEL PRICK test.
Responsible for 1 in 100 deaths from Sudden Infant Death Syndrome (SIDS).
HMG-CoA reductase is under negative feedback control by what?
Mevalonate, cholesterol and bile salts.
What are the two main bile salts?
Glycocholate and taurocholate.
How are cholesterol esters synthesised?
Synthesised in the plasma from cholesterol and the acyl chain of lecithin via lecithin: cholesterol acyltransferase (LCAT).
Synthesised intracellularly from long chain fatty acyl CoA species via acyl CoA acyltransferase (ACAT).
What is the purpose of converting cholesterol to cholesterol esters?
More hydrophobic so pack more tightly in the cores of lipoproteins.
How does ATP synthase work?
The C subunits of the F0 unit rotates when H+ flows through. The gamma unit of F1 also rotates as it is attached. The alpha and beta subunits of F1 are stationary as they are bound to the b subunit of F0, which is bound to subunit a in the membrane.
Which apoprotein on chylomicrons is key to activating lipoprotein lipase?
C-II.
What happens to the products when chylomicrons interact with lipoprotein lipase?
Glycerol: liver for gluconeogenesis.
Fatty acids: beta-oxidation.
Describe gluconeogenesis, starting with pyruvate.
Pyruvate –> oxaloacetate (pyruvate carboxylase)
Oxaloacetate –> phosphoenolpyruvate (phosphoenolpyruvate carboxykinase)
Phosphoenolpyruvate is converted to fructose 1,6 bisP.
Fructose 1,6 bisP –> fructose 6 phosphate (fructose 1,6 bisphosphatase)
Fructose 6 phosphate –> glucose 6 phosphate
Glucose 6 phosphate –> glucose (glucose-6-phosphatase)
Describe post-translational modifications of glutamate.
Modified to generate gamma-carboxyglutamate.
Addition of carboxyl introduces an increased affinity for Ca2+, needed for clotting.
Warfarin works by inhibiting this post-translational modification.
