NAM Flashcards
What are catabolic pathways?
Where food molecules are broken down into small building blocks for biosynthesis. They produce useful forms of energy and heat in this process. These pathways mainly occur in the cytosol.
What are anabolic pathways?
When small molecules are made into larger molecules that form cells. This process requires energy. These pathways mainly occur in the mitochondria.
What is the definition of metabolism?
A series of enzyme reactions within cells for converting fuel molecules into ‘useful energy’ as well as the enzyme reactions of synthesis/breakdown/interconversion of essential biomolecules.
What is the equation for conversion of glucose to CO2 and what pathways act together to do this?
C6H12O6 + 6O2 -> 6CO2 + 6H2O + 30ATP
Glycolysis and TCA cycle act together.
Why do mitochondria have a double membrane?
- In order to maintain a gradient.
- In order to have organised protein complexes than can channel electrons.
Why are fatty acids bound to proteins in the body? Which proteins do they bind to?
- Free fatty acids are not good for you so they bind to proteins.
- In the blood they bind to albumin and in the cells they bind to fatty acid binding protein.
What are the three components of ATP?
1) Phosphate
2) Sugar
3) Nucleotide base adenine
In which pH range is ATP chemically stable?
pH 6-9
What is the formula for ATP hydrolysis?
ATP + H2O -> ADP + Pi + H+
What are the functions of ATP?
- Used directly in cell motility and contraction.
- Used in Na/K pumps, active transport systems and metabolic control.
- Used in metabolism and to add Pi to metabolic intermediates.
What are endergonic and exergonic reactions?
Endergonic = when energy is absorbed in a reaction.
Exergonic = when energy is released in a reaction.
How can the rate of an enzyme reaction be regulated?
- By altering the availability of the substrate to the cell.
- Increasing the amount of enzyme present in the cell by increasing the rate of transcription.
- Interconversion of active and inactive forms of key enzymes.
What do metabolic reactions require?
- Fuel molecules
- Enzyme catalysts
- Cofactors
For what does ATP act as a cofactor for?
Kinase enzymes
How much energy is released in the breakdown of ATP?
31 kJ of energy per mol of ATP
What are UTP, CTP and GTP cofactors for?
- UTP = drives the synthesis of complex sugars.
- GTP = drives the synthesis of proteins.
- CTP = involved in lipid synthesis.
What are oxidation and reduction?
- When a substance is being oxidised, it is losing its electrons to something else i.e. losing a hydrogen atom which is made up of a H+ and an electron.
- When a substance is reduced, it is gaining electrons i.e. a hydrogen atom.
These tend to happen together as redox reactions, one substance steals electrons from the other.
What type of reaction is going from a double bond to a single bond?
Reduction reaction. This is because you add hydrogen atoms to compensate for the lost bond.
Why is a more reduced molecule better at producing ATP than a less reduced one?
Because being more reduced means that the molecule contains more electrons that it can give away. These electrons then go into the electron transport chain where ATP is make. More electrons means more ATP.
What type of cell relies entirely on anaerobic metabolism and why?
Red blood cells because they do not contain any mitochondria.
Why is glucose dangerous when it is not controlled?
It is a highly reactive molecule that can react with proteins. This is what happens in diabetes with high blood glucose. The ring structure of glucose is caused when it reacts with itself.
What are the Fischer and Haworth projections of glucose?
- Fisher = D-glucose linear form.
- Haworth = D-glucopyranose ring form.
What are the three sources of glucose for glycolysis?
- Sugars and starch from diet.
- Breakdown of stored glycogen from the liver.
- Recycled glucose from lactic acid, amino acids or glycerol.
What is the summary, location and function of glycolysis?
Summary = glucose C6 -> 2x pyruvate C3.
Location = cytosol.
Function = energy trapping by formation of ATP. Is also forms some intermediates for fat and amino acid synthesis.
Is glycolysis an oxidation or reduction reaction?
Oxidation
What are the four stages of glycolysis?
1) Activation
2) Splitting of 6C sugar in half
3) Oxidation
4) Synthesis of ATP
Describe the three reactions that occur during the activation stage of glycolysis.
- Glucose is converted to glucose 6-phosphate with the help of ATP and hexokinase/glucokinase. Addition of a phosphate. This reaction is irreversible.
- Glucose 6-phosphate is converted to fructose 6-phosphate by phosphoglucose isomerase.
- Fructose 6-phosphate is converted to fructose 1, 6 biphosphate by phosphofructokinase. Addition of a second phosphate from ATP. This reaction is irreversible.
What are the products of the activation stage of glycolysis?
2ADP and one fructose 1, 6 biphosphate.
What happens during the splitting stage of glycolysis?
Fructoses 1, 6 biphosphate is split into glyceraldehyde 3-phosphate and dihydroxyacetone phosphate by aldolase.
These products are more stable than their fructose origin.
What is the role of triose phosphate isomerase in the splitting stage of glycolysis?
It ensures that you can make glyceraldehyde 3-phosphate from dihydroxyacetone phosphate (the products of splitting) and vice versa. This ensures the correct products are formed so the rest of the pathway can go in the right direction.
Describe the oxidation step of glycolysis.
Glyceraldehyde 3-phosphate goes to 1, 3-biphosphoglycerate with the help of glyceraldehyde 3-phosphate dehydrogenase. NAD+ and Pi are also converted to NADH and H+ simultaneously. The Pi is given to the molecule forming a biphosphate.
What does NAD stand for?
Nicotinamide Adenine Dinucleotide
What do you need to make NADH and H+ from NAD+?
H+ and two electrons.
Describe the ATP synthesis stage of glycolysis.
- 1, 3-biphosphoglycerate is coverted to 3-phosphoglycerate with the help of phosphoglycerate kinase. This reaction produces one ATP.
- 3-phosphoglycerate is converted to 2-phosphoglycerate with the help of phosphoglycerate mutase.
- 2-phosphoglycerate is converted to phosphoenol pyruvate with the help of enolase. This reaction produces one water molecule.
- Phosphoenol pyruvate is converted to pyruvate with the help of pyruvate kinase. This reaction produces an ATP. This reaction is irreversible.
What are the final products of the ATP synthesis stage of glycolysis?
Pyruvate and four ATP molecules because this reaction is happening twice.
What is the net yield of ATP from glycolysis?
2 ATP because the early activation stage uses up two ATP.
What happens to pyruvate in anaerobic glycolysis?
Pyruvate is converted to lactate in order to convert the cofactor NADH back to NAD+ so it can be re-used for more glycolysis. This reaction is catalysed by lactate dehydrogenase.
pyruvate + NADH + H+ → NAD+ + lactate
What happens to pyruvate in microorganisms?
It is converted to ethanol.
What happens to pyruvate when there is excess calorie intake?
It is converted to acetyl CoA which is converted to fatty acids for storage.
Why is glycolysis a major source of ATP in the brain?
Because the cells in the brain are incapable of using fat as fuels.
How can you increase the rate of glycolysis?
- Intense muscle workout and exercise.
- After a high carbohydrate meal (high insulin levels).
- AMP increasing the activity of phosphofructokinase.
How can you decrease the rate of glycolysis?
- By entering a fasting state with high levels of circulating glucagon.
- Feedback inhibition acting on the reaction of fructose 6-phosphate to fructose 1, 6-biphosphate. There is allosteric control of the enzyme phosphofructokinase by ATP and citrate.
What happens in the TCA cycle?
Oxidation of acetyl CoA to carbon dioxide and water along with the production of ATP.
How many different molecules are used in the TCA cycle?
8, therefore 8 reactions.
What is the most vital molecule for the continuation of the TCA cycle?
Oxaloacetate
What is the link reaction?
A reaction that links glycolysis to the TCA cycle: pyruvate + CoA -> acetyl CoA and CO2 catalysed by pyruvate dehydrogenase. One NADH is formed.
What are the cofactors for the link reaction?
- Thiamin pyrophosphate
- Lipoic acid
- FAD
- Coenzyme A
- NAD+
Describe reaction 1 in the TCA cycle.
Oxaloacetate + Acetyl CoA -> Citrate catalysed by citrate synthase.
This is a condensation reaction.
Describe reaction 2 in the TCA cycle.
Citrate -> Isocitrate catalysed by aconitase.
This is an isomerisation reaction.
Describe reaction 3 in the TCA cycle.
Isocitrate -> α-ketoglutarate catalysed by isocitrate dehydrogenase.
One CO2 is lost in this reaction and one NADH is formed making this reaction an oxidation.
Describe reaction 4 in the TCA cycle.
α-ketoglutarate -> succinyl CoA catalysed by ketoglutarate dehydrogenase.
One CO2 is lost and one NADH is formed making this an oxidation reaction.
Describe reaction 5 in the TCA cycle.
Succinyl CoA -> succinate catalysed by succinate thiokinase.
One GTP is formed and one CoA is lost.
Describe reaction 6 in the TCA cycle.
Succinate -> fumarate catalysed by succinate dehydrogenase.
One FADH2 is formed from FAD.
Describe reaction 7 in the TCA cycle.
Fumarate -> malate catalysed by fumarase.
One H2O is consumed in this reaction.
Describe reaction 8 in the TCA cycle.
Malate -> oxaloacetate catalysed by malate dehydrogenase.
One NADH is formed making this reaction an oxidation reaction.
What does FAD stand for?
Flavin adenine dinucleotide
How does the reoxidation of NADH to NAD+ occur?
By transfer of 2H to the carriers of the cytochrome chain (electron transport chain).
Where is the electron transport chain found?
In the inner mitochondrial membrane (the matrix).
What are the products of the reduction of one NADH?
One H2O and three ATP.
What is the overall energy yield of the electron transport chain?
3 x NADH = 2.5
1 x FADH2 = 1.5
1 x GTP
Makes 10 ATP
What are the three enzyme steps that are highly exergonic and irreversible in the TCA cycle?
- Citrate synthase (reaction 1)
- Isocitrate dehydrogenase (reaction 3)
- Ketoglutarate dehydrogenase (reaction 4)
What can also happen to oxaloacetate and α-ketoglutarate?
They can leave the TCA cycle and undergo transamination to form aspartate and glutamate respectively.
Apart from aspartate, what can oxaloacetate also be used to form?
Phosphoenol pyruvate catalysed by PEP carboxylase. This can then be used to make glucose.
What can citrate be used to form outside the TCA cycle?
Fatty acids and sterols.
What can malate be used to form outside the TCA cycle?
Pyruvate catalysed by malic enzyme.
The longer fatty acids are, what consistency do they have?
Longer is more solid, shorter is more liquid.
What is a fatty acid?
A hydrocarbon chain ending in =O, -OH
What are the biological functions of lipids?
- Components of cell membranes (phospholipids and cholesterol)
- Precursors to hormones
- Long term fuels (triglycerides)
What is a triglyceride fat?
Three fatty acids joined together by one glycerol group.
How are stored triglyceride fats broken down in adipose tissue?
1) Lipase (activated by adrenaline and glucose) cleaves off one fatty acid to form DAG (diacylglycerol).
2) Lipase cleaves off another fatty acid to form MAG (monoacylglycerol).
3) Lipase works once more to separate the final fatty acid from the glycerol.
Where do fatty acids and glycerol go when they are broken down by lipase?
- Glycerol diffuses in the blood to all tissues.
- Free fatty acids travel in plasma bound to albumin and act as fuel for muscle, heart and liver.
What are the two ways in which glycerol can be metabolised?
- In most tissues it enters the glycolysis pathway.
- In the liver and in starvation, it enters the glycolysis pathway but it converted to glucose by gluconeogenesis.
Where do all the reactions for fatty acid metabolism occur?
Within the mitochondrial matrix.
How are long-chain fatty acids activated?
With activating enzyme (cytosol), energy from one ATP and CoA reacting with the fatty acid to form a fatty acyl-CoA.
How is fatty acyl-CoA transported through the outer and inner mitochondrial membranes into the mitochondria?
CoA is cleaved off and carnitine is added forming long-chain acylcarnitine which is transported through the CPT1 channel in the outer membrane.
It then passes through CACT in the inner membrane.
What happens to long-chain acylcarnitine when it is within the mitochondrial matrix?
It goes back to fatty acyl-CoA with the help of CPT2 (carnitine is removed).
How many reactions are required for fatty acid metabolism (beta oxidation pathway?
Four
What are the key features of the four reactions in fatty acid metabolism?
1) Removal of two H atoms in the form of FADH2.
2) Addition of water.
3) Removal of two H atoms in the form of NADH and H+.
4) Removal of a 2C unit in the form of Acetyl CoA.
What happens to the fatty acyl-CoA when it has finished its first beta oxidation pathway?
It comes out two carbons shorter than it started. It then re-enters the cycle and keeps losing carbons.
How much product will one 16C fatty acid produce?
8x Acetyl CoA and 7x NADH and FADH2.
What is the ATP yield from the 8 Acetyl CoA that is produced by fatty acid metabolism of a 16C carbon?
The 8 acetyl CoA goes into the TCA cycle and forms 80 ATP.
The 7 NADH and FADH2 enters the electron transport chain and produces 28 ATP.
80 + 28 -2 = 106
What happens to fatty acids with an odd number of carbons?
The chain is elongated using hydrogen carbonate and ATP forming a methylmalonyl CoA. Vitamin B12 is then used to form succinyl CoA which can enter the TCA cycle.
What regulates the lipase enzyme?
Adrenaline and glucagon.
What are the three points of regulation of fatty acid metabolism?
1) The release of fatty acids from adipose tissue.
2) The rate of entry of fatty acids into mitochondria via the carnitine shuttle.
3) The rate of reoxidation of cofactors NADH and FAHD2 by cytochrome/respiratory chain.
Under what circumstances would you see AMP in muscles?
When the demand for energy is high but the supply is low. ADP is converted to AMP instead of ATP to ADP.
What is the difference between hexokinase an glucokinase?
They both catalyse the same reaction (glucose to glucose-6-phosphate) but hexokinase is more general, glucokinase being used specifically for glucose. It has a high Km for glucose so it only works in the liver when glucose levels are high. This is the opposite for hexokinase.
What glucose transporter is found on muscle cells?
GLUT4 - it is insulin-dependent.
How do you make UDP glucose?
By combining glucose-6-phosphate and UTP catalysed by transferase.
How is a glycogen molecule formed?
UDP-glucose is added to a protein primer called glycogenin. This is catalysed by glycogen synthase and involves the loss of UDP. This continues with multiple UDP-glucose molecules until you have a massive branched molecule.
What enzyme catalyses the branching of glycogen?
Branching enzyme
How is glycogen synthase regulated?
By phosphorylation by protein kinase and ATP. When it is phosphorylated, it is inactive.
What dephosphorylates and consequently activates glycogen synthase?
Protein phosphatase
What catalyses glycogen breakdown?
Glycogen phosphorylase
What is the role of the debranching enzyme?
It removes glucose units from the branched regions allowing glycogen phosphorylase to attack the straight chain regions.
What happens to glucose when it is released from the glycogen molecule?
It is released as glucose-1-phosphate. Mutase enzyme converts it to glucose-6-phosphate where it is then converted to glucose by glucose-6-phosphatase in the liver only.
Why is muscle unable to provide glucose into the bloodstream for metabolism?
It does not have glucose-6-phosphatase so it is unable to make glucose. Instead, glucose-6-phosphate goes straight into glycolysis for energy.
How is glycogen phosphorylase regulated?
It is active when it is phosphorylated by protein kinase.
It is inactive when dephosphorylated by protein phosphatase.
How is protein kinase activated?
- A first messenger activates a G-protein coupled receptor.
- The receptor activates adenylyl cyclase increasing the amount of cAMP inside the cell.
- cAMP then causes inactive cAMP-dependent protein kinase to become active.
- cAMP-dependent protein kinase then catalyses the reaction protein + ATP -> protein kinase + ADP.
What is the effect of insulin on glycogen enzymes?
- Glycogen synthase becomes dephosphorylated and active.
- Glycogen phosphorylase becomes dephosphorylated and inactive.
What is the effect of adrenaline and glucagon on glycogen enzymes?
- Glycogen synthase is phosphorylated and inactive.
- Glycogen phosphorylase is dephosphorylated and active.
What happens when glucose levels are high in the liver?
Glucose binds to glycogen phosphorylase and inactivates it.
What happens to glycogen phosphorylase in muscle during contraction?
- Ca is released into the sarcoplasmic reticulum.
- Ca binds to the calmodulin domain of glycogen phosphorylase kinase activating the enzyme.
- This in turn activates glycogen phosphorylase causing glycogen to be degraded providing energy for the contracting muscle.
What are the effects of AMP and ATP on glycogen phosphorylase?
- AMP is an allosteric activator of the enzyme.
- ATP is an allosteric inhibitor.
What is von Gierke’s disease?
A glycogen storage disease affecting glucose-6-phosphatase. Causes enlarged liver and hypoglycaemia.
What is Pompe’s disease?
A glycogen storage disease affecting lysosomal glycosidase causing muscle weakness and cardiac failure.
What is McArdle’s disease?
A glycogen storage disease affecting glycogen phosphorylase causing exercise intolerance.
What is a condition associated with high levels of uric acid?
Gout
How much protein is it recommended for a person to eat per day?
0.75g of protein per kg of body weight.
What happens when a person takes in more protein then they require?
The surplus amino acids are rapidly catabolised and the nitrogen is excreted as urea in the urine. Very high intake can cause kidney damage.
What should the nitrogen balance be in normal healthy adults?
The intake should be equal to the amount excreted i.e. the rate of protein synthesis is equal to the rate of degradation.
What is the pathway of degradation for most cellular proteins?
They are recognised as old and damaged and are removed by the ubiquitin breakdown system.
What is the pathway of degradation for foreign exogenous proteins?
They are taken into vesicles by endocytosis or autophagocytosis where the vesicles fuse with the lysosome. Here, proteolytic enzymes degrade the proteins into amino acids.
What is transamination?
Where an amino acid reacts with a keto acid to form a different amino acid and different keto acid - their amine groups have swapped.
What is oxidative deamination?
Amino acid + H2O + coenzyme -> Keto acid + ammonia + coenzyme-2H
Degradation of amino acids.
What is transdeamination?
Where there is a transfer of an amine group from one compound to another (transamination) but also the loss of the amine group in the form of ammonia (deamination). Both of these steps are found within the same reaction.
What is the fate of keto acids after amination reactions?
They enter the TCA cycle as pyruvate or other citric acid components and are used as a source of ATP.
In starvation, the carbon skeletons 13 amino acids can be converted to glucose by the liver. These amino acids are classified as glucogenic.
What are ketogenic amino acids?
AAs that can only be degraded into acetyl CoA. This then goes into the TCA cycle or forms fat. These AAs are leucine and lysine.
What are the roles of the liver in nitrogen metabolism?
- Removal of amino acids, glucose and fats from the portal blood supply.
- Absorbs amino acids used for synthesis of cellular proteins.
- Synthesises plasma proteins.
- Synthesises haem, purines and pyrimidines for DNA.
- Undergoes transdeamination to degrade excess AAs.
- Converts ammonia to urea for excretion.
How are amino groups transported in the bloodstream and why?
As glutamine because it is more efficient as it can carry two amino groups.
What happens to glutamine in the liver?
It is converted to glutamate where one ammonia is released.