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Biochem II > Enzymes & metabolism > Flashcards

Enzymes & metabolism Flashcards

1
Q

What happens when glucagon binds to a GPCR?

A

The G-protein subunit is activated (binds GTP) and in turn, activates adenylyl cyclase. Adenylyl cyclase will start converting ATP to cAMP. cAMP binds to PKA and subunits dissociates and are thus activated. PKA phosphorylates the protein with PFK-2 activity, causing FBPase-2 activity instead. This lowers levels of fructose 2,6-biphosphate in the cell. Fructose 2,6-biphosphate is a strong activator of PFK-1, which is the enzyme that does the reaction that brings fructose-6-phosphate into glycolysis. When f2,6BP levels are low, PFK-1 activity is very low and glycolysis is thus inhibited (Glucagon = we don’t want to break down glucose)

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2
Q

What happens when insulin binds to GPCR?

A

Inhibits FBPase-2 activity promoting PFK-2 activity -> more F26BP -> higher PFK-1 activity -> fructose-6-phosphate into glycolysis

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3
Q

Whats needed for glycolysis?

A

NAD+, ATP, glucose

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4
Q

ATP-dependent/generating steps in glycolysis

A

Glucose -hexokinase-> glucose 6-phosphate
Fructose 6-phosphate -PFK-1->fructose 1,6-biphosphate
1,3-biphosphoglycerate -phosphoglycerate kinase->3-phosphoglycerate
Phosphoenolpyruvate -pyruvate kinase->pyruvate

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5
Q

Phosphofructokinase-1 (PFK-1)

A

Important regulatory step for entering glycolysis. Regulated allosterically by fructose 2,6-biphosphate, inhibited allosterically by high levels of ATP. Citrate and PEP also inhibits

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6
Q

Substrate level phosphorylation

A

Soluble enzymes and chemical intermediates phosphorylate something instead of membrane bound chemicals / transmembrane gradient

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7
Q

Phosphoenolpyruvate (PEP)

A

Pyruvate kinase will remove phosphor group from PEP to form pyruvate.

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8
Q

Pyruvate kinase

A

Catalyzes the last step of glycolysis. Inhibited allosterically by high levels of ATP, acetyl-CoA. In liver, cAMP can phosphorylate and inactivate it

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9
Q

Which enzyme breaks down glycogen?

A

Glycogen phosphorylase

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10
Q

Important enzymes in gluconeogenesis

A

Pyruvate carboxylase, PEP carboxylase, FBPase-1, glucose 6-phosphotase

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11
Q

Regulation of gluconeogenesis

A

Pyruvate carboxylase requires acetyl-CoA as positive effector. AMP strongly inhibits FBPase-1

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12
Q

Molecules needed for gluconeogenesis

A

4 ATP, 2 GTP, 2 NADH, pyruvate/acetyl-CoA

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13
Q

PFK-2/FBPase-2

A

Protein with dual enzymatic activity depending on PKA activation/inactivation (not phosphorylated; PFK-2 -> formation of fructose 2,6-biphosphate) (phosphorylated; FBPase-2 -> breakdown of F26BP to F6P)

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14
Q

Phosphorylase b kinase

A

activation of glucogen phosphorylase (b -> a) by phosphorylating 2 places. Activated by glucagon in liver and [AMP] in muscle

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15
Q

PP1 (phosphorylase a phosphotase)

A

Inactivation of glucagon phosphotase by removal of phosphate groups. Activated by insulin

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16
Q

Glucogen activation cascade

A

Epinephirne or glucagon binds to CPCR. G-protein activates adenylyl cylase, leading to rise in cAMP. cAMP activates PKA, which activates phosphorylase b kinase, which activated glycogen phosphorylase (b->a). This starts the breakdown of glycogen to glucose 1-phosphate

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17
Q

What is the Pyruvate dehydrogenase complex (PDH)?

A

Oxidizes pyruvate into acetyl-coa and co2

18
Q

Important regulatory steps in citric acid cycle

A

Regulation at three steps (Pyruvate->Acetyl-CoA, Acetyl-CoA->citrate among others)
PDH complex: allosteric inhibition by ATP, acetyl-coa and NADH, allosteric activation by CoA, NAD+ and AMP. Phosphorylation by E1 inhibits (kinase is allosterically activated by ATP).
Citrate formation: allosteric inhibition by NADH, citrate, ATP, succinyl-CoA
Generally allosteric inhibition by later products in pathway

19
Q

Whats needed for beta-oxidation

A

Something that stimulates breakdown of fatty acids, FAD and NAD+, movement of fatty acids into mitochondria

20
Q

Products of beta-oxidation

A

Acetyl-CoA, FADH2, NADH, protons

21
Q

Regulation of beta-oxidation

A

Shuttle of fatty acids from cytosol into mitochondria, high level of NADH

22
Q

What is ketone bodies?

A

When the body need energy from the liver, after acetyl-CoA is produced in beta-oxidation, it can be converted to ketone bodies, transported in the blood and then when it enters other tissues, it can be converted back to Acetyl-CoA and enter citric acid cycle

23
Q

What is the chemiosmotic theory?

A

That the movement of protons to the intermembrane space from the matrix by the electron transport chain “fuels” the ATP generation by using the transport of protons back to the matrix to generate ATP

24
Q

What is needed for oxidative phosphorylation?

A

O2, NADH, FADH2, H+

25
Q

What complexes are part of the ETC?

A

Complex I (NADH:Ubiquinone oxidoreductase/NADH dehydrogenase), Complex II (Succinate Dehydrogenase), Complex III (Cytochrome bc1 complex/ubiquinone:cytochrome c ocidoreductase), Complex IV (Cytochrome oxidase)

26
Q

Describe the action of Complex I

A

Transfer of a hydride ion from NADH and a proton from the matrix to a Ubiquinone (Q) and the transfer of four protons from the matrix to the intermembrane space. The electrons are transferred from Fe-S centers to ubiquinone. QH2 then diffuses to complex III

27
Q

Describe the action of Complex II

A

Transfer of electrons from succinate to FAD, through Fe-S centers and then to ubiquinone. No pumping of protons take place here. QH2 then diffuses to complex III

28
Q

Describe the action of Complex III

A

Transfer of electrons from QH2 to cytochrome c and transfer of protons from matrix to intermembrane space. Two molecules of cytochrome c is reduced for every QH2. 4 protons are pumped from the matrix to intermembrane space.

28
Q

Describe the action of Complex IV

A

Transfer of electrons from cytochrome c to O2 and the movement of four protons to intermembrane space. O2 is reducted to H2O. 4 cytochrome c are needed for one reduction of O2, meaning intermediates need to be tightly bound as they are ROS.

28
Q

What is the proton motive force

A

When protons flow down their electrochemical gradient, te electrochemical energy drives the synthesis of ATP from ADP and P.

29
Q

Connection between ATP synthase and ETC

A

The ETC is responsible for the electrochemical gradient that ATP synthase needs to produce ATP, and ATP synthase is responsible for moving H+ back into the matrix so that is not too energy consuming for complex I, III and IV to pump out protons.

30
Q

Regulation of oxidative phosphorylation

A

Rate of [ADP]. If the pH in cell drops, IF1 will prevent the ATP synthase from producing ADP from ATP.

31
Q

How is the urea and citric acid cycle connected?

A

alpha-ketoglutamate is an important protein in both; amino groups are often transferred here to form glutamate which can enter the mitochondria and lose amino group

32
Q

What is NADH?

A

NADH is an electron carrier. NADH specifically is an electron donor and a reductive agent

33
Q

What is NAD+?

A

NAD+ is an electron carrier. NAD+ specifically is an electron acceptor and a oxidative agent

34
Q

How do you experimentally determine Km and kcat?

A

Steady state kinetics. Low [E] high [S] measure change in absorbance? Measure initial volocity and use Michealis-Menten kinetics to calculate Km and using that, kcat.

35
Q

Why is urea an excellent molecule for nitrogen excretion?

A

Water soluable. High nitrogen density for such a small molecule

36
Q

How is ATP synthesis continued under hypoxic conditions?

A

The lactic acid pathway doesn’t require oxygen. Pyruvate can be turned into lactate which regenerated NAD+ for glycolysis

37
Q

How does the liver assist muscles during hypoxia?

A

Lactate gets transported to liver cell where it can be turned back into glucose (cori cycle). The liver can also assist the muscles by decreasing glucolysis, increasing glycogen breakdown and gluconeogenesis

38
Q

Describe three similarities between photophosphorylation and oxidative
phosphorylation of ADP to form ATP.

A

Both use ATP synthase, and both ATP synthases are powered by a proton gradient. Both are dependant on redox-reactions and both has an electron transport chain

39
Q

Which metabolic pathways take place in the mitochondria?

A

Citric acid cycle, Oxidative phosphorylation, Beta-oxidation

40
Q

What protein complex is responsible for the generation of the PMF in chloroplasts?

A

cytochrome b6f complex

Biochem II (4 decks)

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