Midterm 2 quizzes Flashcards
A case study: A 20-year-old subject reports that he feels severe muscle cramp after strenuous exercise. Blood glucose test reveals normal blood glucose level in the patient. What is your guess about this patient’s diagnosis?
Type V: Muscle phosphorylase deficiency (McArdle’s Disease):
The second messenger cAMP activates cAMP-dependent protein kinase by
By dissociating the catalytic subunits from regulatory subunits
Name the two enzymes in glycogen metabolism which are activated by dephosphorylation.
glycogen synthase and PP1
Hormonal control of glycogen breakdown is necessary in muscle tissue to quickly generate energy in stress. What is the role of similar control in liver tissue?
Hormonal control is done in emergency situations. This release of epinephrine will trigger the whole g protein thing. Dietary emergency. During this time glucagon is released and does the same thing as epinephrine but in liver. This happens to regulate blood glucose. Epinephrine works on liver as well and blocks glycogen synthesis to make sure we have sufficient glucose in the blood
What is the role of phosphpoprotein phosphatase-1 in control of glycogen metabolism?
Controlling the glycogen breakdown; once emergency has passed its role is to inhibit enzymes
Name the enzyme, which is activated by Ca ++ in Glycogen metabolism
Phosphorylase kinase. If it is phosphorylated then it is super active in the presence of a small amount of calcium
What is the difference between glycogen and starch and whatis the significance of this structure?
Starch is not very branched and is not soluble. Glycogen is more branched, it is dissolved and does not cause auto immune problems. Glycogen can also be catabolized fast
We can eat lot of starch and we do not have any problem. Why do children with defect in branching enzyme have severe problem?
Anything going through the digestive tract is digested and then absorbed. The starch is converted into glucose before it is absorbed. If starch is synthesized in the liver it is recognized as a foreign particle and is attacked by autoimmune system which causes inflammation.
Case study: A child (3year old) is diagnosed with severe liver disorder and inflammation in the liver. Tissue biopsy reveals presence of large glycogen granules in liver. What do you think is wrong in this patient?
Type IV: Branching enzyme deficiency (Anderson’s Disease): This is the presence of starch like granules. This has to do with the branching enzyme. There are not enough branches which makes it starch like and insoluble. This causes the inflammatory response
Phosphorylated Glycogen phosphorylase (“a”, the active form) is independent of allosteric effectors. Explain need for such regulation
This happens under emergency situations. It is phosphorylated and becomes super active. It is independent of allosteric effectors. Gets activated under hormonal control. In this situation you dont care about anything except your job
Name the enzymes which are substrates for c-AMP-dependentprotein kinase.
Phosphorylase kinase, glycogen synthase, PP1 inhibitor, bottom of g subunit of PP1
What critical enzymes of glycogen metabolism are activated by insulin-stimulated protein kinase?
Insulin activated under happy conditions. PP1 is activated by insulin. PP1 will activate glycogen synthase (indirect activation by insulin)
What effect a good dose of coffee will have on glycogen metabolism?
Coffee has caffeine. Caffeine inhibits cyclic nucleotide phosphodiesterase so it doesnt break down CAMP and PKA will be constantly be active. Now glycogen breakdown will be unable to stop which leads to hyperkinetic situation
How does Epinephrine affect the activity of Phosphorylase kinase?
Epinephrine leads to activation of phosphorylase kinase. Epinephrine activates receptor, which activates gprotein, which activates adenylyl cyclase, which activates PKA, which activate phosphorylase kinase
How does cAMP affects the activity of phosphoproteinphosphatase-1? Explain.
The cAMP will activate PKA which will phosphorylate the bottom side g-subunit of PP1 thereby shutting it down
What are the end products of pentose phosphate pathway?
NADPH, CO2, GAP, F6P
What is the need for pentose phosphate pathway?
To produce NADPH for reducing power. It produces a 5C intermediate (pentose phosphate) which is necessary for nucleotide synthesis
People with defective GPDH enzyme are resistant to malaria. Why?
First enzyme in pathway. If this isnt working properly, people are not able to produce NADPH which helps protect us against free radicals. Malaria parasite is very sensitive to these radicals. Therefore if you dont have functioning enzyme then you dont have NADPH, then you have lots of radicals, then you are resistant to malaria. This is an issue when you eat flava beans which has a toxin. Also big problem when you take anti malaria drug
What enzymes are responsible for the production of NADPH and pentose phosphate?
Glucose 6 phosphate dehydrogenase, 6-phosphogluonolactonase, 6-
What are the other enzymes involved in pentose phosphate pathway? Why are they needed in this pathway?
Isomerization and epimerization reactions = ribulose 5 phosphate
d. None of the above is correct statement.
b. Pentose phosphate pathway can be directly linked to glycolysis.
What are the substrates and end products of pentose phosphate pathway?
G6P, NADP+ -> GAP, F6P, NADPH+H
Hexokinase is upregulated (i.e. present in high amount) in cancer cells?
Hexokinase is first enzyme in metabolism. This is because cancer cells are crazy and need lots of pentose sugar so that they can divide really quickly. Therefore they need a lot of glucose 6 phosphate that is made by hexokinase
c. Calculate the G for this reaction in forward direction if concentration of oxaloacetate is 1x 10-8 M, malate 0.2 mM, and NAD+/NADH ratio in rat liver mitochondria is 10.
a. This reaction will proceed in the backward directionbecause it is super endergonic.
b. Insulin generally promotes anabolic pathway i.e. synthesis of glycogen then why should it activate PDC?
a. Phosphoprotein phosphatase 1, pyruvate dehydrogenase complex, glycogen synthase
What side reaction would take place if E1 subunit is separated from PDC?
E1 is as good as pyruvate decarboxylase in alcoholic fermentation. End product here is acetaldehyde which is no good. Same thing can happen as a side reaction with E1. Therefore aldehyde may be produced and be bad if it is not taken up immediately by E2
Which of the dehydrogenases have FAD cofactor?
Succinate dehydrogenase (substrate), alpha ketoglutarate dehydrogenase, PDC (covalently bound)
How many oxygen molecules are used for the complete oxidation of glucose to CO2 during Glycolysis, PDC and citric acid cycle pathway?
Start with 6 C glucose and by the end every C is turned into a CO2. NO OXYGEN WAS USED. The oxidizing agents were NAD+ and FAD
Where do the additional 6 oxygen atoms come from, to generate 6 molecules of carbon dioxide?
All of them come from water
How many grams of glucose is needed to elevate an object of 50 Kg to the height of 100 meters. Assume that all the energy released by ATP hydrolysis is used with 100% efficiency in this work, and G = - 50KJ/Mole in physiologicalcondition.
how much energy is needed to lift the object?:
Deficiency of thiamine or arsenate poisoning lead to the similar symptoms and mostly brain functions are affected in these diseases. Why?
The brain uses aerobic glucose catabolism for energy and the PDC enzyme is really
Which enzymes are affected by thiamine deficiency?
PDC, alphaketoglutarate dehydrogenase complex
How many net ATP molecules are produced by substrate levelphosphorylation during complete catabolism of one glucose molecule?
glycolysis makes 2 ATP and 2 GTPs are made in citric acid cycle. Therefore 4 total
CAC is referred as amphibolic pathway Why?
Each of the 8 compounds are siphoned off to make other things. There is a catabolic component (break down of pyruvate into CO2) but there are also anabolic parts (intermediates are used to make other things in the cells)
Write down the different forms of energy at various steps in the oxidative phosphorylation i.e. NADH oxidation coupled to ATP generation.
NADH acts as a strong reducing agent and coq10 is oxidizing agent. During oxidation reactions, the free energy is used to change in the conformation of the complex which will cause the pumping of protons. Therefore oxidizing energy changes to confirmational energy to electrical potential energy. Then proton gets into ATP synthase where the turbine will move so kinetic energy. This will change the alpha beta subunit of ATP synthase which is conformational energy and then turns it into chemical energy in the form of ATP
How many Co-enzyme Q10 molecules will be needed to oxidize one molecule of NADH, or one molecule of FADH2
One. Coq10 can accepts 2 electron and NADH/FADH can give 2 electrons
Fe++/Fe+++ plays major role in the transfer electrons from one molecule to other during mitochondrial ETC and many complexes and proteins have either Fe-S centres or heme rings, but Fe++ in each protein has different reduction potential. Why?
Although all have same element (iron), depending on the electron cloud around it when it is complexed in a protein. If there is dense electrons around it then it will low reduction potential. If there is a small electron cloud around it then it will have a high electron potential
Inner mitochondrial membrane is present as involuted making cristae like structures. Why?
Folds increase surface area. All of the ETC machinery is located in the membrane. The more surface area, the more area where ETC can happen and therefore more energy can take place
How many complexes does electrons from NADH go through before reaching Oxygen?
3 (complex 1/3/4)
Why do electrons have go through multiple steps (or carriers) before being accepted by Oxygen?
Step by step leads to a controlled release of free energy. This prevents changes in temperature and pressure that would happen in combustion. All of the energy release can be harvested
How many cytochrome c molecules are reduced during transfer of electron from one Ubiquinone (QH2) in complex III?
Two
Reduction of coenzyme Q takes place in
complex 1, 2 and 3
Rotenone and antimycin A inhibit NADH dehydrogenase (complex I) and Ubiqinone oxidase (complex III) respectively. Which one is more potent and dangerous poison?
Antimycin A because it inhibits a later complex in the electron transport chain. There is less bypassing in this situation therefore there will be a smaller gradient
iv. Reduction of Oxygen
Yes synthesis of ATP
- electricity
Water = H+
What is Q cycle?
In complex 3. It is the cycle of oxidation and reduction of coq10. 1 electron is transfered ultimately to cytC. 1 electron is transfered back to coq10. Overall there will be a pumping of 2 electrons from the matrix into the intermembrane space (indirectly)
Free energy released during the oxidation of NADH or FADH2 is used synthesize ATP (phosphorylation). How are these two reactions coupled? Is it direct or indirect? Explain.
It is indirect coupling. Prove this by adding the substrate of one reaction doesn’t allow for both reactions to go. You need the substrates of both. Also if you inhibit oxidation, there will also be no ATP synthesis. If you stop ATP synthesis, you will see that oxidation reactions also stopped. Can uncouple this using small molecules that can destroy the gradient
c. How many grams of net ATP and CO2 will be produced?
a. 342 g = 1 mol sucrose = 2 glucose = 4 alcohol. 4x 46=184 g alcohol. Alcohol relative density is 0.8. 184/0.8 = 230 mL -> 0.23 L 0.23/10 = 0.023 x 100 = 2.3 %
Name all the kinases involved in glycolysis
Hexokinase, phosphofructokinase-1, pyruvate kinase, phosphoglycerate kinase (4)
Name the substrates in forward direction of each kinase reaction.
Glucose, F6P, 2 phosphoglycerate, 1,3 bisphosphoglycerate
Name the reaction involving oxidation-reduction reaction in glycolysis.
glyceraldehyde 3 phosphate dehydrogenase
Which compound is reduced in the reaction in reaction
NAD+ is reduced into NADH
How many reactions of glycolysis involve phosphoryl group transfer? Provide the names of enzymes.
Six. 2 require ATP (hexokinase and phosphofructokinase). 4 have ATP involved (hexokinase, pfk, pyruvate kinase, phosphoglycerate kinase). GAPDH adds phosphate with no ATP, phosphoglycerate mutase also doesnt require ATP involved.
Which reaction in glycolysis is responsible for the net gain of ATP during this pathway?
glyceraldehyde 3 phosphate dehydrogenase (coupled with phosphoglycerate kinase)
Name the reactions in glycolysis involving phosphate group transfer without any involvement of ATP or ADP.
glyceraldehyde 3 phosphate dehydrogenase, phosphoglycerate mutase
Lactic acid, which lowers the pH causing fatigue. There is no ATP production during this step of the reaction. Why should this reaction be there?
To regenerate NAD+ in emergency situations so that we can allow the last 4 steps of glycolysis to persist at a fast pace and produce ATP.
reaction?
Nucleophilic attack on carbonyl carbon by the sulfur from sulfhydryl group on cysteine from active site of enzyme
Despite the low amount of ATP generated during glycolysis. Why this is the preferred pathway in muscle during fast movement?
Because it is substrate level phosphorylation and we can produce lots of ATP by catabolising glucose. Aerobic conditions cannot be accelerated at this rate. It is accelerated 100x
c. This reaction does not require ATP hydrolysis.
a) Phosphatase chops of phosphate and the enzyme becomes inactive
Why is glucose phosphorylated in the first step of glycolysis?
We do not want glucose to leave the cell. Glucose is phosphorylated by ATP to become gluose-6-phosphate, which now is charged. This charge does not allow it
positive. How does this reaction proceed in forward direction?
It is coupled to reaction 7 which is very exergonic, the product is immediately taken up by reaction 7
glycolysis?
phosphofructokinase
The substrate cycle is also called futile cycle, Why?
Occurs when two metabolic pathways run simultaneously in opposite directions
Is futile cycle really a futile exercise? If not what is the importance of this cycle.
It is used to control the flux of glycolysis.
iii. In both the lactate DH and alcohol dehydrogenase reaction during homolactic and alcoholic fermentation.
ii. NADH is being oxidized to NAD+
Yeast carry out alcoholic fermentation pathway to
Regenerate NAD+ for glycolysis reactions producing ATP under anaerobic
Why is glucose stored in the form of glycogen in muscle andliver as emergency stock?
Glycogen can be catabolized very fast into glucose and can be metabolized to make lots of ATP
What is the difference between glycogen and starch and what is the significance of this structure?
They are both polymers of glucose, they both have chains of 1-4 linkage and 1-6 linkage
What is the name of the cofactor in Glycogen phosphorylase reaction
Pyridoxal phosphate that is covalently linked to the enzyme
What kind of nucleophilic substitution takes place in glycogenphosphorylase reaction? Provide evidence for your answer
It is an SN1 reaction, meaning one step at a time. The leaving nucleophile is substituted with the attacking nucleophile. We know this because of the presence of a carbocation semi chair intermediate. Also there is no confirmation change between substrate and product. When gluconolactone, a similar product was added, then the reaction was inhibited.
Phosphorylated Glycogen phosphorylase (“a”, the active form)is independent of allosteric effectors. Explain need for such regulation
It is activated via phosphorylation of its two dimer parts. It is phosphorylated by phosphorylase kinase. This happens under emergency conditions where we need to produce lots of glucose 6 phosphate and ATP. These emergency conditions are triggered by epinephrine and glucagon. Even in the presence of ATP and glucose 6 phosphate it will still stay active. It will also ignore AMP.
Hormonal control of glycogen breakdown is necessary in muscle tissue to quickly generate energy in stress. What is the role of similar control in liver tissue?
The liver does not need to generate ATP to do anything. The liver makes sure there is sufficient glucose in the blood. The liver will break down glucose and secrete it into the blood. The emergency that the liver can work on but muscles can’t is the situation in which a person has not eaten for a long time and blood glucose levels are dropping. This is called a dietary emergency.
What is the mechanism of Phosphoglucose mutase reaction?
Enzyme is phosphorylated. It lends its phosphate to the 6th carbon, then replenishes the phosphate with the one on the 1st carbon
Why is Glucose 6 Phosphatase dephosphorelated (removal of phosphate) in liver?
Glucose 6 phosphate is charged and cannot be secreted into the blood. Therefore we dephosphorylate it to neutral glucose so that it can be secreted into the blood to maintain blood glucose levels.
What are the two enzymatic activities og debranching enzyme?
First one is glycosidic transferase. Second is a 1,6 - glycosidase.
