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Flashcards in Metabolism Deck (104):

What is an exergonic reaction?

Reaction where ΔG∘'


What is an endergonic reaction?

Reaction where ΔG∘' > 0


Why is the process of coupling a reaction?

For a reaction to be feasible, only overall ΔG∘' needs to be -ve. This means that a reaction with +ve ΔG∘' can be coupled with much more -ve ΔG∘' reactions in order to make them feasible, since overall ΔG∘' would be -ve.


What is a 'state function'?

A function that will be the same no matter what pathway is taken, so long as the initial and final states are the same.


What are the associated ΔG∘' values for hydrolysis of ATP?

ATP + H2O → ADP + Pi (-30.5 KJ mol^-1)
ATP + H2O → AMP + PPi (-45.6 KJ mol^-1)
PPi + H2O → 2Pi (-19.2 KJ mol^-1)


Why is ATP the universal energy currency?

- ATP hydrolysis is exothermic and is coupled with the majority of endothermic metabolic reactions in order to make them feasible.
- ATP synthesis is endothermic and is coupled with the majority of exothermic metabolic reaction. It acts as an energy carrier between endothermic and exothermic reactions.


Why is ATP hydrolysis so exothermic?

1. ADP and Pi have more resonance stabilisation, so are more stable and in a lower energy state than ATP.
2. There is more electrostatic repulsion between phosphate groups in ATP compared to ADP and Pi.
3. More water is able to bind to ADP and Pi in order to stabilise them by hydration.


What is the implication of a very -ve ΔG∘' on K?

A very -ve ΔG∘' indicates a very large K, so position of equilibrium lies far to the right in favour of product formation.


What is the implication of a very +ve ΔG∘' on K?

A very +ve ΔG∘' indicates a very small K, so position of equilibrium lies far to the left in favour of reactants.


What is the phosphorylation potential?

The ΔG∘' that occurs when a phosphorylated compound is dephosphorylated by hydrolysis.


What is the significance of the phosphorylation potential?

A compound with a more -ve phosphorylation potential is capable of phosphorylating a compound with a less -ve phosphorylation potential.


Why does ATP not have a very -ve phosphorylation potential?

1. In order to ensure that energy is released in small packets as not to damage cells.
2. In order to ensure that it can be phosphorylated relatively easily by other biological compounds (eg phosphocreatinine).


What is the benefit of having 2 separate redox systems for energy production and biosynthesis?

- NAD+/NADH used for energy production.
- NADP+/NADPH used for biosynthesis.
- Allows for the 2 processes to be uncoupled from each other.
- NAD+/NADH ratio kept high for oxidation in energy production.
- NADPH/NADP+ levels kept high for reduction in biosynthesis.


What is the role of the liver in fuel metabolism?

- Glucose homeostasis
- Synthesis and storage of triglycerides
- Oxidation of fats and synthesis of ketone bodies
- Nitrogen recycling and amino acid metabolism


What are the heart's preferred fuels?

- Fats
- Ketone bodies


Why does enzyme activity need to be regulated?

1. To avoid futile cycles.
2. To link energy production to usage.
3. To respond to physiological changes in the body (e.g. fasting, exercise).
4. To prevent the build-up of intermediates that take part in side-reactions (feedback inhibition).


What are the physiological states that affect metabolism?

1. Fasting/feasting
2. Short-term exercise
3. Long-term exercise
4. Diabetes mellitus


What are the main functions of glycolysis?

1. Substrate-level phosphorylation of ADP to ATP allows some ATP to be produced in glycolysis, which is especially important in anaerobic respiration when oxidative phosphorylation in aerobic respiration cannot keep up with ATP demand.
2. NADH produced enter the mitochondria and are reoxidised, releasing energy used in oxidative phosphorylation.
3. Produces pyruvate which is further broken down in the citric acid cycle.


What is the overall purpose of steps 1-4 of glycolysis?

Lysis stage. 2 ATP molecules are consumed in order to split the glucose molecule into GAP and DHAP


What is the purpose of isomerisation of G6P into F6P?

In step 4, the mechanism of cleavage for F1,6BP is aldol cleavage, which requires ketone group at C2, hence the isomerisation.


What is the overall purpose of steps 5-7 in glycolysis?

Oxidation stage. Aldehyde groups in GAP are converted to carboxyl groups that are more stable. The energy released from this process is subsequently used to phosphorylate 2 molecules of ADP per GAP.


Why is triose phosphate isomerase (TIM) considered a 'perfect enzyme'?

- Its rate of catalysis is almost instantaneous once all the substrates have bond.
- Increasing the catalytic efficiency of the enzyme has no effect on rate of reaction.
- Rate of reaction only limited by the rate at which the substrate-enzyme complex forms.


What is the overall purpose of steps 8-10 in glycolysis?

Rearrangement stage. C=C and C=O bond in PEP are converted to 2 C=O bonds that are more stable. The energy released from this reaction is used to phosphorylate another ADP to ATP.


What is the overall reaction of glycolysis?

Glucose + 2 ADP + 2Pi + 2 NAD+ → 2 Pyruvate + 2 NADH + 2H+ + 2ATP + 2H2O


What is the purpose of lactate fermentation?

- Glycolysis does not need O2 and is capable of generating 2 molecules of ATP per glucose.
- In doing so, 2 molecules of NAD+ is also reduced to NADH.
- NAD+ eventually gets depleted and glycolysis can no longer occur.
- Lactate fermentation re-oxidises NADH to NAD+, recycling it and ensuring that glycolysis is able to continue.


What are the advantages and disadvantages of anaerobic respiration?

- Advantage: Up to 100 times quicker than aerobic respiration.
- Disadvantage: Much more wasteful than aerobic respiration. Only ~31% of energy used to make ATP. The rest is dissipated as heat.


What is the purpose of the different kinematic properties of hexokinase/glucokinase?

- Hexokinase maintains high activity even when [glucose] is relatively low, which allows muscles to maintain high rate of glycolysis and energy production under such conditions.
- Glucokinase activity is relatively low in low [glucose]. This decreases the rate of glucose metabolism in liver under such conditions, which is good considering the liver is mainly involved with such processes as glycogenesis and fatty acid synthesis, both further reducing blood [glucose].


What is the significance of PFK2?

- PFK2 is a bifunctional enzyme complex with both kinase and phosphotase domains.
- Phosphorylation of cardiac muscle isoform of enzyme causes conformation change that promotes activity of kinase domain and inhibits activity of phosphotase domain.
- Phosphorylation of hepatocyte isoform inhibits kinase domain and promotes phosphotase domain.


What are the control points of glycolysis?

1. Rate of glucose intake into the cell.
2. Rate of phosphorylation of glucose.
3. Rate of phosphorylation of fructose-6-phosphate.
4. Rate of conversion of PEP to pyruvate.


What are the properties of control points?

- Control points are irreversible reactions with large free energy changes. These reactions can only be controlled by changing the activity of the enzyme.
- Other reactions are reversible reactions that accommodate changes in substrate concentration adjust their flux accordingly.


What is the relationship between ATP, ADP and AMP?

- 2ADP ↔︎ ATP + AMP
- Reaction catalysed by adenylate kinase


What are the diameters of glycogen granules in the fast/fed states?

- Fed: >40 nm
- Fast: ~10 nm


What are the major control points of glycogen metabolism?

- Synthesis of glycogen from UDPF by glycogen synthase.
- Hydrolysis of glycogen into glucose-1-phosphate.


What are the effects of the fed state on glycogen metabolism?

- In fed state, intracellular [glucose], [ATP] and [citrate] are high while [AMP] is low.
- PFK1 is inhibited, driving the flux of futile cycle towards F6P.
- This increases intracellular [G6P].
- [G6P] inhibits activity of glycogen phosphorylase and promotes glycogen synthase.
- Insulin also inhibits phosphorylase kinase indirectly (by promoting breakdown of cAMP), thus also inhibits glycogen phosphorylase.
- Insulin promotes glycogen synthase by inhibiting GSK.
- Rate of glycogen synthesis increased.


What are the effects of the fast state on glycogen metabolism?

- In the fast state, blood [glucose] is low, leading to the release of glucagon.
- Glucagon affects liver cells only.
- It promotes glycogen phosphorylase activity by promoting activity of phosphorylase kinase (through phosphorylation by PKA).
- Increase in activity of glycogen phosphorylase increases rate of glycogenolysis and glucose is released from the liver.
- Low blood [glucose] causes decrease in rate of glycolysis, a decrease in [G6P], which also drives glycogenolysis.


What are the effects of short-term exercise on glycogen metabolism?

- In short-term exercise, increase in intracellular [Ca2+] increases the activity of phosphorylase kinase and thus increases glycogenolysis.
- Once all ATP and phosphocreatine is depleted, increase in [AMP] and decrease in [ATP] further promotes phosphorylase kinase activity.


What roles do compartmentation have on regulation of gluconeogenesis?

- PEPCK is located in the the cytoplasm exclusively (in some animals). This means that oxaloacetate needs to be transported out of mitochondria. This is achieved through the malate shuttle whereby oxaloacetate is converted to malate by malate dehydrogenase before being transported out through malate transporter proteins. This ensures that not all oxaloacetate takes part in gluconeogenesis.
- Glucose 6-phosphotase is located in ER. This ensures that not all G6P is converted back to glucose and some can be converted to glycogen.


What is the importance of the cori cycle?

- Allows lactate produced by muscles to be converted back to glucose by gluconeogenesis in the liver and then transported back to muscles.
- Provides glucose for the brain.


What are the reactions feeding into the citric acid cycle?

- Glycolysis
- β-oxidation
- Ketone body metabolism
- Amino acid metabolism


What are the reactions coming out of the CAC?

- Gluconeogenesis
- Fatty acid synthesis
- Oxidative phosphorylation
- Amino acid metaboliam


How is pyruvate transported into the mitochondria?

Pyruvate translocase


What are the benefits of pyruvate dehydrogenase (PDH) being a multienzyme complex?

1. Reduces distance between active sites and increases rate of reaction.
2. Decreased chance of intermediates taking part in unwanted side reactions.
3. Allows for all enzymes in the complex to be easily regulated.


What is the mechanism of PDH action?

- PDH catalyses 5 separate reaction converting pyruvate to acetyl-CoA.
- The intermediates are transferred between the different active sites in the enzyme by a lipoamide arm, allowing the reactions to be coupled to each other.


What is the overall reaction catalysed by PDH?

Pyruvate + CoA + NAD+ → Acetyl-CoA + CO2 + NADH


What is the importance of coupling during link reaction?

Coupling ensures that free energy released from decarboxylation and oxidation of pyruvate is used in the synthesis of NADH and acetyl-CoA.


What are the types of reactions catalysed by PDH?

1. Decarboxylation
2. Oxidation
3. Transfer to CoA


How is PDH regulated?

- Phosphorylation by PDH kinase deactivates it.
- Dephosphorylation by PDH phosphotase activates it.


What are the effects of the fed state on PDH activity?

- In the fed state, high levels of blood glucose results in increased rate of glycolysis and CAC, resulting in more ATP, NADH and acetyl-CoA being produced.
- In muscles, these promote the activity of PDH kinase, thereby inhibiting PDH and decreases rate of link reaction, driving flux towards gluconeogenesis and glycogen synthesis.
- In liver, high blood glucose leads to release of insulin from the pancreas, which promotes activity of PHD phosphotase and increases PDH activity. This increases the rate of CAC, but for the purpose of increasing rate of fatty acid synthesis in the liver.


What are the effects of exercise on PDH activity?

- Exercise increases the rate of glycolysis via upstream regulation, which increases rate of pyruvate production.
- Pyruvate inhibits PDH kinase, increasing activity of PDH and link reaction.
- Muscle contraction during exercise also increases intracellular [Ca2+], which promotes activity of PDH phosphotase, further increasing activity of PDH.
- Increased rate of link reaction increases rate of acetyl-CoA activity and CAC, increasing ATP production.


What is the significance of aconitase reaction?

Carbon moved from carbon 3 in citrate to carbon 2, which is required for the isocitrate dehydrogenase reaction to take place.


What is the significance of α-ketoglutarate dehydrogenase?

- α-ketoglutarate dehydrogenase is very similar in structure to PDH.
- This reflects the fact that the reaction it catalyses in also very similar to the link reaction.


What is the name of the enzyme catalysing reaction ADP + GTP ↔︎ ATP + GDP?

Nucleoside diphosphokinase


What is the significance of succinate → oxaloacetate reaction sequence?

The reaction sequence is a very common oxidation → hydration → oxidation sequence used to convert CH2 group to C=O group.


What is the overall reaction for CAC?

Acetyl-CoA + 3NAD+ FAD + GDP + Pi + 2H2O → 2CO2 + 3NADH + FADH2 + GTP + 2H+ + CoA


What is the overall function of the CAC?

The CAC uses free energy released from the breakdown of acetyl group into CO2 to synthesise NADH and FADH2, which are then re-oxidised to release energy for oxidative phosphorylation.


What is anaplerosis?

The act of replenishing CAC intermediate that have been removed for other metabolic reactions.


What is the importance of anaplerosis?

- CAC intermediates are constantly being removed for use in other reactions (e.g. gluconeogenesis and amino acid synthesis). Carbon is lost.
- Acetyl-CoA is not a source of carbon as it is fully broken down to CO2.
- Other reactions need to constantly replenish carbon lost from CAC in order to maintain constant level of intermediates and efficiency of CAC.


What are the main control points in the CAC?

- Oxaloacetate → Citrate (Citrate synthase)
- Isocitrate → α-ketoglutarate (Isocitrate dehydrogenase)
- α-ketoglutarate → Succinyl-CoA (α-ketoglutarate dehydrogenase)


What is the significance of the purine nucleotide cycle?

- Important anaplerotic pathway used to generate fumarate from aspartate.
- Increases the amount of CAC intermediates present.
- Increases rate of CAC in muscles during exercise.
- Deficiencies is pathway leads to muscle cramping after short periods of exercise.


Why is the link reaction seen as the 'point of no return' for glucose?

- Once pyruvate converted to acetyl-CoA, carbons in acetyl group destined to be broken down.
- Acetyl-CoA cannot take part in gluconeogenesis.


What are the advantages of fats as energy stores?

- They are hydrophobic so don't change osmolality of cells.
- They release more energy per unit mass compared to carbohydrates.


What are the 2 types of lipases?

- Hormone-sensitive lipase (HSL)
- Adipocyte triglyceride lipase (ATL) - Found exclusively in adipocytes


What is the purpose of β-oxidation?

To weaken the bond between the α and β carbon in fatty acyl-CoA so that it can be broken and an acetyl group to be taken off in acetyl-CoA.


How are fatty acids activated?

- Fatty acids are attached to CoA to form fatty acyl-CoA.
- This process is carried out by thiokinases (specific to different lengths of fatty acids) using hydrolysis of ATP to AMP as energy source.


What is the significance of the carnitine shuttle?

- Allows activated acyl-CoAs to be transported into the mitochondria where the β-oxidation enzymes are found.
- Acts as a regulatory set for β-oxidation by compartmentation for β-oxidation. This ensures that the NAD+/FAD in the mitochondria is not all used up by the reaction and prioritises it to the CAC.


What are the enzymes involved in the carnitine shuttle?

- Carnitine acyltransferase I attaches the acyl group onto the carnitine in the cytosol.
- Carnitine acyltransferase II detaches the acyl group from the carnitine in the mitochondrial matrix.


What is the significance of the reactions that convert fatty-acyl CoA into β-ketoacyl-CoA?

It is a sequence of oxidation → hydration → oxidation reactions that convert a CH2 group into C=O group.


What is the overall reaction for the β-oxidation of palmitoyl-CoA?

Palmitoyl-CoA + 7NAD+ + 7FAD + 7 CoA + 7H2O → 8 Acetyl-CoA + 7FADH2 + 7NADH + 7H+


What are the limitations of β-oxidation?

β-oxidation needs more O2 than glucose metabolism. This means that it cannot occur under anaerobic conditions (e.g. in foetus).


What is the significance of citrate synthase regulation?

Promotes gluconeogenesis.


How do mono-unsaturated fatty acids undergo β-oxidation?

If C=C bond between α and β carbons (i.e. in even number position), then the resultant compound may be a natural substrate for enoyl-CoA dehydrogenase. If not (i.e. in odd number position), the double bond can either be isomerised to become normal substrate, or reduced to normal C-C bond.


How do odd-numbered saturated fatty acids undergo β-oxidation?

- The majority of the molecule is hydrolysed to produce acetyl-CoA, leaving propinyl-CoA, which is converted to succinyl-CoA and enters the CAC.


What are the types of fatty acyl-CoA dehydrogenases?

- Very long chain (VLCDH)
- Long chain (LCDH)
- Medium chain (MCDH)
- Short chain (SCDH)


What is the significance of ketone bodies?

They act as a transport form of acetyl-CoA between tissues.


What are the clinical significances of medium chain acyl-CoA dehydrogenase?

- 10% of cot deaths are thought to be due to MCAD deficiency.
-Unripe ackee fruit contains inhibitor of MCAD and is responsible for Jamaican vomiting sickness.


What is the only source of gluconeogenesis from fats?

- Glycerol can be converted to DHAP which then enters the normal gluconeogenic pathway.
- The first enzyme in this reaction is glycerol kinase, which is only present in sufficient amounts in the liver, so glycerol must be returned to the liver.


What are the control points of β-oxidation?

1. Hormone-sensitive lipase
2. Glycerol 3-phosphate: Low glucose leads to low levels of this compound, which is needed for TAG synthesis, leading to release of free fatty acids into the blood to undergo β-oxidation.
3. Carnitine shuttle: Malonyl-CoA is a product of fatty acid synthesis and is an inhibitor of CATI.
4. NAD+/FAD: High rate of CAC would result in low levels of NAD+/FAD for fatty acid synthesis. Compartmentation means that these co-enzymes are prioritised for CAC.


What is the function of the peroxisomes?

- Mitochondria cannot oxidise fatty acids >22 carbons long.
- Peroxisomes break down fatty acids to shorter chains and then supplies them to mitochondria.


What are the functions of the different peroxisomal proliferation activated receptors (PPARs)?

1. PPAR-α: Upregulates fatty acid oxidation in liver and muscles.
2. PPAR-γ: Helps adipose tissues store fat.
3. PPAR-δ: Promotes oxidation in fats and muscles.


Where does fatty acid synthesis take place?

- Cytoplasm.
- Acetyl-CoA needs to be transported out of the mitochondria into the cytoplasm. This is carried out by citrate shuttle.


What is the sequence of events that take place in citrate shuttle?

1. Citrate is transported out of mitochondria by tricarboxylate transport system.
2. In the cytoplasm, ATP-citrate lyase converts citrate into oxaloacetate and acetyl-CoA by hydrolysing ATP.
3. Oxaloacetate is converted to malate by malate dehydrogenase.
4. Malic enzyme converts oxaloacetate into pyruvate (releasing NADPH and CO2).
5. Pyruvate transported into the mitochondria through pyruvate translocase.
6. Pyruvate converted to oxaloacetate by pyruvate carboxylase.
7. Oxaloacetate converted back into citrate by citrate synthase, with addition of acetyl-CoA.


How is acetyl-CoA converted to malonyl-CoA?

- Acetyl-CoA carboxylase (ACC).
- CO2 is fixed into acetyl-CoA with energy from hydrolysis of ATP.


What is the significance of malonyl-CoA and NADPH in fatty acid synthesis?

- Malonyl-CoA provides acetyl-CoA equivalent, but its decarboxylation provides free energy for the addition of an acetyl group onto the growing fatty acyl-CoA.
- NADPH provides reducing potential.


What is the enzyme responsible for fatty acid synthesis?

- Fatty acid synthase.
- Large multi-enzyme complex with multiple domains to catalyse multiple reactions.


How does fatty acid synthesis terminate?

Fatty acid drops off fatty acid synthase when it is ~16 carbons long (palmitate).


What are the fates of fatty acids once they have been synthesised?

1. Elongation
2. Desaturation
3. Synthesis of triglycerides


What are the types of ACC present?

- ACC1: Found in liver and adipose tissues only, involved in fatty acid synthesis.
- ACC2: Found in tissues that oxidise fatty acids but don't necessarily synthesis them (e.g. skeletal muscle). They synthesis malonyl-CoA in order to regulate β-oxidation.


What are the ways by which fatty acid synthesis is controlled?

1. Malonyl-CoA synthesis: ACC1 is inhibited by AMPK directly through phosphorylation, which is activated by high [AMP] and upstream kinases from PKA pathway. It is activated allosterically by citrate and inhibited allosterically by acyl-CoA.
2. High acetyl-CoA in mitochondria drives flux towards fatty acid synthesis.
3. Glucose is needed in the synthesis in the glycerol 3-phosphate, which is needed to synthesis TAGs. Low glucose results in low rate of TAG synthesis.
4. Compartmentation: In the fed state, when blood glucose high, rate of glycolysis and CAC high, producing lots of NADH and ATP that allosterically inhibit CAC enzymes. This leads to increase in [citrate] and promotes citrate shuttle. When [citrate] is low, citrate shuttle activity is low, so acetyl-CoA prioritised for the CAC.


Where are TAGs synthesised and stored in the body?

- TAGs are synthesised in the liver.
- They are transported to adipose tissue in LDLs bound to Apo-B proteins and stored there.


What are the non-glucogenic amino acids?

- Leucine
- Lysine


Which amino acids can be converted to glutamate and then α-ketoglutarate?

- Arginine
- Glutamine
- Histidine
- Proline


Which amino acids can be converted to succinyl-CoA?

- Isoleucine
- Methionine
- Threonine
- Valine


Which amino acids can be converted to fumarate?

- Phenylalanine
- Tyrosine


Which amino acids can be converted to pyruvate?

- Alanine
- Cysteine
- Glycine
- `Serine
- Threonine
- Tryptophan


Which amino acids can be converted to acetyl-CoA?

- Isoleucine
- Leucine
- Threonine
- Tryptophan


Which amino acids can be converted to acetoacetyl-CoA?

- Leucine
- Lysine
- Phenylalanine
- Tryptophan
- Tyrosine


What are the principles behind amino acid metabolism?

- The nitrogens are removed and excreted via urea cycle.
- Carbon backbone used in energy production (either through CAC or ketone bodies)


Which prosthetic group is a vital part of amino transferase function?

- Pyridoxal phosphate
- Acts as 'parking spot' for amino groups


What is the function of the glucose-alanine cycle?

- Amino acids are converted to keto acids to be used in respiration in tissue (e.g. muscles).
- Amino groups on these amino acids are transported in the form of alanine in the blood to the liver, in combination with pyruvate.
- In the liver, the alanine is deaminated to pyruvate and the amino group is excreted as urea.
- Pyruvate undergoes gluconeogenesis in the liver and is transported back to muscles as glucose in blood.


How are amino groups carried by glutamate in the liver?

1. Glutamate is combined with ammonium to glutamine in muscles by glutamine synthetase (via γ-glytamyl phosphate intermediate and using energy from ATP hydrolysis).
2. Glutamine is transported to the liver in blood.
3. In the liver, it is broken down into glutamate by glutaminase.
4. Ammonium group released enters urea cycle and is excreted as urea.


What is the process of carbamoylphosphate formation?

2ATP + NH3 + HCO3- → NH2-CO-O(PO4)3- + 2ADP + Pi


How is ammonia added to the urea cycle?

1. Carbamoylphosphate (2ATP)
2. Alanine (1ATP)


How is the urea cycle linked to the urea cycle?

1. When glutamate is deaminated, it becomes α-ketoglutarate, which is a CAC intermediate.
2. Argino-succinate, a urea cycle intermediate, can be converted to fumarate. This is called the aspartate-arginosuccinate shunt.


How is the urea cycle controlled?

- On demand.
- The rate of the urea cycle is increased when [Glu] increases as a result of amino acid metabolism.