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Flashcards in Tony O'sulivan Deck (88):

What is the most important catabolic pathway?

- starch degregation.


What do systems under anaerobic conditions do to pyruvate?

- reduce pyruvate to lactate or ethanol.
- in the process oxidises NADH to NAD+.


What is the product of the first stage of glycolysis?
What is required?

1,6 bisphosphate



Why is ATP required in step 1 of glycolysis?

Addition of polar hydrophilic phosphate groups prevents metabolites difrfting out through the cell membrane.

Addition of charged phosphates allows enzymes to bind with higher affinity.

>> glucose is moved in and out of cells via a uniportor.
- when phosphorylated it is trapped & no longer be transported out of the cell.


What enzyme is required in step 1 (production of Glucose-6-phosphate) of glycolysis what does it do?

- hexokinase
- uses a complex with ATP and Mg2+ substrate.
- the binding of glucose causes a conformational change (induced fit).


What happens once G 6-phosphate is formed? What enzyme catalysts the next reaction?

Converted to fructose-6-phosphate (F-6P) a heroes sugar.
- catalysed by phosphoglycose isomerase.


What happens to the F-6P that was just formed?

- the second committed step occurs.
F-6P is phosphorylated by ATP. Forming fructose 1,6 bisphosphate.
> catalysed by fructokinase a tetrameric enzyme.


What is special about the tetrameric enzyme phosphofructokinase?

- it has alosteric properties and shows sigmoid all binding curve.
- ATP binds to binding site and another site away from the actie site inhibiting the enzyme.


How do other sugars enter the glycolytic pathway?

- via phosphorylation.
> galactose and fructose are the 2 other most important sugars.


At what stages of the cycle do galactose and fructose enter the cycle?

- Galactose enters at the point of Glucose 6P
- fructose enters at Frucotse 6P


When does stored carbohydrate in the form of starch enter the glycolytic pathway?

Via glucose-1-phosphate


Describe the structure of intracellular starch.

- degregation is used to metabolise carbohydrate stores in cells such as liver and muscles.
- chains have a alpha 1-4 linkage. The branch structure produces lots of free non-reducing ends.


What is the product of intracellular starch degradation?

- generates phosphorylated hexose sugar directly.


What enzyme catalysed the phosphorylitic cleavage of liner starch polymers? How does it work?

- glycogen phosphorylase.
- Works in with a starch detracting enzyme that removes the alpha 1-6 branches in animal glycogen and plant amylopectin.


In order to feed into glycolysis the starch must be converted in to glucose 6-phosphate what is the enzyme that catalysed this reaction? What is the mechanism?

- phosphoglucomutase.
- similar mechanism to the enzyme that converts 3&2 phosphoglycerate
- the active form of the enzyme is phosphorylated by catalytic amounts of the intermediate glucose 1-6 bisphosphate.
- phosphate is de-Phosphorylated and re-Phosphorylated at the position on serine.


What is glycolysis?

The sequence of reactions that metabolites one molecule of glucose to 2 molecules go pyruvate with net production of 2 ATP.


What happens in stage 2 of glycolysis?

- splits 6-carbon sugar into 2 3-carbon sugars


What is the step that is catalysed by the enzyme aldose? What else is produced in this reaction?

The conversion of fructose 1-6 bisphosphate (from step 1) to Glygeraldehyde 3-phosphate (GAP).

The reaction also produces Dihydroxy-acetone phosphate (DHAP)


what happens to the dihydroxyacetone phosphate? What enzyme catalysed this reaction?

Using the enzyme >>>>> triose phosphate isomerase.


Explain some of the special features of the triose phosphate isomerase enzyme.

- one of the most catalytically active enzymes known; rates of catalysis approach the theoretical limit. Said to be 'catalytically perfect'.
- the enzyme is ESSENTIAL for the efficient energy production in glycolysis.
- deficiencies in this enzyme are associated with sever neurological disorder - TPI deficiency. Characterised with haemolytic anemia.


What else is important about DHAP?

- it is also a precursor for glycerol
- this reaction a;sows glycerol (produced by hydrolysis of lipids and fats) to enter the glycolytic pathway and be used to produce ATP.
- the reactions can also run in the opposite direction to glycerol for lipid biosynthesis in this direction the formation of ATP does not occur.


What are the stages that convert glycerol into DHAP?

- glycerol is converted to l Glycerol 3-phosphate by the enzyme GLYCEROL KINASE >> ATP is converted to ADP in the process.
- l glycerol 3- phosphate is converted to the desired DHAP by the enzyme GLYCEROL PHOPHATE DEHYDROGENASE.


What is stage 3 of glycolysis?

It generates eneergy in the form of ATP production.
- The 'core' of glycolysis.
- stage also results in the oxidation of the sugars coupled to the reduction of NAD+ to NADH.
- 2 steps here's ATP is produced


How is ATP produced in stage 3?

- using a phosphorylated sugar with high phosphoryl group transfer potential to phosphorylate ATP.


What is the oxidation step e.g. Step 1 of stage 3 of glycolysis?

- the production of 1,3- bisphophoglycerate
- the oxidation of Glygeraldehyde-3-phosphate (GAP) is coupled to the phosphorylation of inorganic phosphate.


What catalyses the conversion of GAP to 1,3 - bisphophoglycerate?


The step uses NAD+ and Pi
Produces NADH and H+


How is this reaction (step 1 of stage 3 of glycolysis) central to glycolysis?

- generates a compound containing a phosphoryl group with a high transfer potential without involving ATP.
> although DG for overall process is v negative the phosphorylation step by itself would have a large D+ve.


If the phosphorylation step would be largely negative delta G how is the step able to take place?

- favourable redox is used to drive unfavourable phosphorylation.
- a covalent enzyme intermediate links oxidation to phosphorylation (catalyses).


What is the first ATP producing step (stage 3 glycolysis step2), what happens to 1,3-BGP?

- phosphorylation by 1,3 BGP occurs.
- uses ADP
- causes the production of 3- phosphoglycerate


What enzyme catalyses the reaction of 1,3 Bisphosphoglycerate to 3-phosphoglycerate?

- Phosphoglycerate kinase


How does the phosphoglycerate kinase enzyme work?

- Phosphoryl group attached to the carboxyllic acid group in 1,3- BGP has a high transfer potential and can phosphorylate ADP in a reaction thermodynatimically favoured in vitro.


What is stage 3 step 3 of glycolysis?

Generation of a second compound with a high phosphoryl gourd transfer potential.
3-phosphoglycerate is converted by 2 enzymes into phosphoenolpyruvate.


What catalyses the reaction of 3-Phosphoglycerate to 2-phosphoglycerate?

- Phosphoglycerate mutase.
- it acts by generating a phosphorylated enzyme using 2,3 BPG


What enzyme catalyses the reaction from 2- phosphoglycerate to phosphoenolpyruvate?

- Enolase
- Enolase uses dehydration (removal of H2O) to form a C=C double bond.


Hey does phosphenolpyruvate have a high phosphoryl group transfer potential?

- due to the presence of C=C double bond, with hydroxyl (OH) group attached making it an enol.


What is the second ATP production step? (Stage 3 step 4 of glycolysis)

- phosphorylation of phosphenolpyruvate.
- ADP + H+ produces ATP.


What enzyme catalyses stage 3 step 4 of glycolysis?

- pyruvate kinase catalyses the production of Pyruvate by the phosphaprylation of ADP to ATP in the theromodynamically favoured reaction.



What are the overall result of the glycolytic pathway?

- One molecule of glucose is oxidised to 2 molecules of pyruvate.
- 2 molecules of NAD+ are reduced to 2 NADPH
- 2 molecules of ATP are used in the production of fructose 1,6 bisphosphate.
- 4 molecules of ATP are produced by phosphorylation of ADP as 2 3-carbon sugar molecules pass through stage 3 of the cycle.
>>> net gain = 2 ATP


What is the overall reaction of glycolysis?

- GLUCOSE + 2Pi + 2ADP + 2NAD+ >>>>>> 2 PYRUVATE + 2STP + 2NADH +2H+


What is the conversation of pyruvate to lactate in anaerobic muscles catalysed by and use up?

- catalysed by lactate dehydrogenase and uses NADH.
- produces lactate and NAD+.


What is the reaction for the conversation of glucose to lactose?

- GLUCOSE + 2Pi + 2 ADP >>> 2LACTATE + 2ATP.


What happens in the Cori Cycle?

- lactose is converted back into something useful.
- in mammals lactate is transported back to the liver where it is converted back to pyruvate by LDH in Cori cycle
- can then be converted back to glucose in glycogenesis.
> this cycle consumes ATP.


What does the conversation of pyruvate to ethanol require?

- carried out by many microorganism so.
- reactions use NADH and are catalysed by pyruvate decarboxylase and alcohol dehydrogenase.


What does the pyruvate decarboxylase enzyme catalyses the reaction of?

- Pyruvuve H+ goes in and CO2 comes off.
- this produces acetaldehyde.


What does the enzyme alcohol dehydrogenase catalyses the reaction of?

- the conversion of Acetaldehyde to ethanol
- uses NADH + H+ goes to NAD+.


Under aerobic conditions what happens to both NADH and Pyruvate?

- used in further stages of energy generation.
- compleate oxidation of glucose to CO2 + water yields many more molecules of ATP per glucose than glycolysis & thus is potentially more efficient.


What findings suggest that glycolysis is an ancient metabolic pathway?

- because many aerobic metabolism is often 'bottled on' to a common anaerobic pathway.


why must glycolysis be so tightly controlled?

- essential for cellular homeostasis.
- levels of common intermediates must be kept roughly constant to allow totality of metabolic process to function correctly.
- the supply of pyruvate limits further aerobic energy generation.


What is the main control point of the glycolytic pathway?

- first common irreversible step, the phosphorylation of Frucotse-6-phosphate to fructose 1,6-bisphosphate.


How is the formation of glucose1-phosphate from starch by phosphorylase controlled?

- by feedback inhibition of ATP.


Where does glycolysis occur within the cell?

- within the cytoplasm.
- complexes allow local concentrations of intermediates to differ from bulk cellular concentrations- necessacery to account for thermodynamics


Where does stage 2&3 of energy generation occur?

- in cytoplasmic compartment of aerobic prokaryotes, but carried out in specialised organelles such as the mitochondria in eukaryotic cells.


In Eukaryotes what occurs inside the mitochondria?

-- respiratory chain (inner membrane)


In Eukaroytes what occurs in the Matrix of the mitochondria?

- the citric acid cycle
- pyruvate oxidation


What happens in the citric acid cycle?

- the products of gylcolylis are fully oxidised to CO2.
- simmultaneously generating reduced co-factors: NADH and FADH.
- does not however generate ATP.
> it is the processes occurring across the inner mitochondrial membrane that generate ATP from reduced co-factors.


What is the first step of the TCA cycle? (How does this step merge with fat oxidation?)

- pyruvate is oxidised to an activated intermediate Acetyl CoA.
- One C atom is lost as Co2.
- Acetyl CoA is also produced by oxidation of fats and thus the process of lipid catabolism and carbohydrate catabolism is linked at this point.
- the oxidation of pyruvate generates the co-factor NADH


Explain the role of pyruvate dehydrogenase.

- catalyses the oxidation of pyruvate.
- the dehydrogenase consists of 3 different enzymes and 5 co-enzymes.
> the Acetyl group from pyruvate is attached to a carrier molecule CoA. This sis catalysed by Dihydrolipoyl transacetylase.


What is the overall equation of the formation of Acetyl co-a from pyruvate?

Pyruvate + CoA + NAD+ >>>>> Acetyl + CO2 + NADH + H+.


What are the 3 distinct steps of the mechanism of the pyruvate dehydrogenase where pyruvate is converted into Acetyl-co-a

1. Decarboxylation: TPP is combined with the pyruvate and decarboxylated in order to yields hydroxyethyl-TPP.
2. Oxidation: the hydroxyethyl group is transferred to lipoma die whcih is lipoid acid derived that links to the side chain of a lysine residue by an aside linakge. Creating an energy rich thioester bond. Disufide group of lipoamide acts as an oxidant and is reduced.
Hydroxyethyl-TPP + lipoamide >>> TPP + acetyllipoamide
3. Acetyl CoA is formed when the Acetyl group is transferred from acetyllipoamide. As the group is transferred the energy rich thioester bond is preserved.

The final step of this reaction occurs when the oxidised from of lipoamide is regenerated by (E3). 2 e- are transferred to NAD+ producing NADH.


What is Berberi and what is it caused by?

- It is a vitamin defficiency disorder characterised by neurological and cardiac symptoms due to a shortage in vit B (thymine) in the diet.
> thymine is required for the production of TTP.
- nervous tissue requires glucose rather than fats as a source of metabolic fuel. Defficiencies in pyruvate dehydrogenase activity due to lack of cofactor present prevent pyruvate being converted into Actyl CoA.
- this causes a build up of pyruvate in the blood.
- nervous system becomes damaged due to failure in generation of ATP for anaerobic metabolism.


What are the other sources of CoA?

Derived form dietary lipids by hydrolysis.
- major energy source in humans as more energy is derived from fats than sugar.


How is the intracellular of fatty acids carried out?

- hydrolysis of triglycerides is carried out by lipases regulated by hormones via signal transduction systems.


Where does fatty acid oxidation occur?

- within the mitochondria & generates reduced co-factors which can produce ATP via oxidative phosphorylation.
- the end product of fatty acid oxidation is Acetyl CoA.


Where else other than in the mitochondria can fatty acid oxidation occur?

- within peroxisomes in which no reduced co-factor is produced. And energy is dissapated as heat.
- end product is still Acetyl co-a


What is the ultimate achievement of the TCA cycle?

- takes in 2 Acetyl CoA and oxidises them to CO2.
- in the process eneergy is generated in the form of reduced Co factors.


What is step one of the TCA cycle? What is the reaction catalysed by?

C2 + C4 >>>> C6.
- the 2 carbon Acetyl group from Acetyl co-A is added to a 4 carbon organic acid oxaloacetate. This reaction produces citrate.
- catalysed by citrate synthase. It exploits the high transfer potential of the Acetyl group attached to co-enzyme A.


What type of reaction is step 1 of the TCA cycle?

- a condensation reaction followed by hydrolysis to give CoA.
- conformational changes in the enzyme as the reaction proceeds prevents hydrolysis of citryl CoA and protects intermediates from reaction with the solvent.


What is the second step of the TCA cycle?

C6 >>>>> C5 + CO2 + NADH (first oxidation)
- citrate is isomerised to isocitrate in a process catalysed by aconitase.
- the reaction moves the hydroxyl group into the correct position
- next oxidative decarboxylation is catalysed by isocitrate dehydrogenase. Oxidation of at the C2 of isocitrate gives an unstable intermediate, oxalosuccinate which looses CO2 to form the 5C alpha-Ketoglutanate.


What is step 3 of the TCA cycle? (Second oxidation)

- C5 >>>>> C4 + CO2 + NADH
- alpha-ketoglutanrate is converted to succinylcholine COA by oxidative decarboxylation reaction catalysed by alpha-ketoglutarate dehydrogenase (similar in structure to pyruvate dehydrogenase).


What is step 4 of the TCA cycle?

- GTP formation.


How is succinylcholine CoA used to produce GTP?

- Succinyl CoA is an activated intermediate with a high group transfer potential (for succinate)
- the transfer of the Succinyl group is linked to phosphorylation of GDP to GTP by inorganic phosphate.
> the reaction is catalysed by Succinyl CoA synthetase.


GDP is usually phosphorylated but ATP an also act as an acceptor, WHY?

- GDP and ATP are inter convertible by nucleotide diphosphokinase.
- GTP + ADP >>>>>> GDP + ATP


Break down better step 4 of TCA cycle.

- Succunyl CoA form Succinyl phosphate by the displacement of CoA.
- the phosphate is then transferred to GDP via enzyme linked phosphate intermediate.


What is the final step 5 of the TCA cycle (3rd and 4th oxidations)?

To complete the cycle succinate is oxidised back to OXALOACETATE in 3 steps.


What is part i of step 5 of TCA cycle?

I. Succinate is oxidised to fumarate, forming C=C double bond, in a reaction catalysed by succinate dehydrogenase; FAD is reduced to FADH2. Whereas other citric acid enzymes are soluble, SD membrane associated and linked to ETC.


What is part ii step 5 of the TCA cycle?

Water is added to C=C double bond in fumarate to from maleate in a reaction catalysed by fumarase.


What is part iii of step 5 of the TCA cycle?

- Malate is oxidised to oxaloacetate in a reaction catalysed by Malate dehydrogenase.
> NAD+ is reduced to NADH.


What is the difference between the outer and inner membrane of mitochondrion?

- outer = highly permeable with proteins called porins giving access to larger molecules.
- inner = very limited permiability. - vital for energy generation; oxidative phosphorylation occurs across it.


What are the 2 distinct faces of the inner membrane referred to as?

- the Martix side (in) or N side (-ve)
- cytoplasmic site (out) or P side (+ve).


What is mt DNA?

- mitochondria retain a residual bacterial genome.
- cells contain multiple mitochondria which each contain circular DNA molecules (mtDNA).
MtDNA is inherited cytoplasmically (I.e. Material inheritance).
- the residual mitochondrial genome only has limited coding capacity.
- they've lost the capacity for independent replication and reply on products from nuclear genes for many functions.


How does oxidative phosphorylation generate ATP?

- ATP is formed as e- are transferred from NADH or FADH2 to oxygen by a series of e- carriers.
- the intermediate sources that power ATP synthesis are proton gradient and the electrical potential energy across the membrane.


What is the name given to the proton gradient and eclectic potential energy across the membrane?

- The proton-motive force.


What happens to the co-factor NADH?

NADH >>> NAD+ + H+ (this reaction gives to electron to an electron carrier reducing it).
- Reduced electron carrier >>> 2e- + oxidised e- carrier ( the reduced electron Carrier donates its 2e- to 1/2 O2 + 2H+ producing water.


Explain how coupling the proton motive force to chemiosmosis ultimately helps to produce ATP.

- proton motive force is generated by stepwise movement of e- by e- carriers whcih leads to the pumping of protons OUT of the mitochondrial matrix.
- Oxidation of NADH & phosphorylation of ADP are coupled by the generation of a proton gradient.
- as protons travel via ATP synthase back into the cell.


How is energy released gradually in the ETC?

- most free energy released when glucose is oxidised to CO2 is retained in the reduced co-factors NADH and FADH2.
- Respiration: e- are released from NADH and FADH2 to oxygen:
- it is released gradually to maximise APT production as free energy is released in small increments by the ETC.


What is the equation showing the transfer of e- to oxygen from reduced co-factor NADH?

NADH + H+ + 1/2O2 >>>>>>>>>> NAD+ + H2O


What is the ETC made up of?

- 4 multi protein complexes.
- 3 of these are e- driven proton pumps that create a proton gradient.
- transfer of e- down this chain is driven by redox potential.


How do redox reactions power transmembrane ion pumps in the mitochondria?

- e- can be transmitted from one half reaction to another via protein conductors- works best if proteins are close together & cannot move much relative to one another. I.e. In complexes for multifunctional proteins embedding the proteins in a membrane makes e- transfer more efficient & helps prevent the 'loss' of e- to solution.