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Biochem > Unit 13 > Flashcards

Unit 13 Flashcards

1
Q

What is the function of glycogen in mammals? In what tissues does it occur?

A
  • The function of glycogen in mammals is the storage form of glucose. When it is stored this way, the osmotic nature of the cell doesn’t change
  • Occurs in the skeletal tissue or liver
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2
Q

Using structures, write a balanced chemical equation for the reaction catalyzed by glycogen phosphorylase

A

Draw it

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3
Q

Explain why glycogen phosphorolysis is energetically more efficient than hydrolysis. Think about this in terms of the product of glycogen phosphorolysis and what would be required to produce a similar molecule using glycolysis

A

Glycogen phosphorylsis is energetically more efficient than hydrolysis becaues it adds a phosphate to glucose making it glucose 1 phosphate. This can interconvert with glucose 6 phosphate which could be used for glycolysis. This saves ATP because you can directly get G6P instead of adding Pi to a glucose molecule

  • Hydrolysis would just break the bond without adding a phosphate group
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4
Q

List several reasons why sugar nucleotides are suitable substrates for biosynthetic reactions

A
  1. Formation is irreversible because it produces PPi which is hydrolyzed
  2. Nucleotides contribute to delta G of binding (at the active site, the nucleotides can form all these non-covalent interactions with the enzymes and helped to contribute to enzyme catalysis)
  3. Nucleotide is a good leaving group
  4. Separates hexoses (glucose, fructose) that are meant for synthesis from those that are required for energy.oxidation or other paths in general
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5
Q

Using structures, write a balanced chemical equation for the reaction that generates a sugar nucleotide. Name the other product of the reaction and discuss why it is important

A

*Draw this
- Generates pyrophosphate in the process which will be broken down by pyrophosphatase. This essentially makes the reaction irreversible due to Le Chatelier’s Principle

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6
Q

Using structures, write a balanced chemical equation for the reaction by glycogen synthase

A

*Draw this
Tips: The nonreducing end of the already made glycogen will attack the alpha carbon of the glucose phosphate 1
*UDP is released

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7
Q

What enzyme elongates the glycogen chain

A

Glycogen synthase

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8
Q

Discuss the biological significance of teh branched structure in glycogen

A
  • The biological effect of branching is to increase the number of nonreducing ends. This increases the number of sites accessible to glycogen phosphorylase and glycogen synthase! (important), both of which act on nonreducing ends.
  • More solubility of the glycogen
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9
Q

What is the significance of non-reducing sites?

A
  • The non-reducing ends is how the glycogen chain can attack the glucose-UDP to add another glucose onto the chain
  • The non-reducing end is where the glycogen phosphorylase will facilitate the attack of a phosphate group for degradation
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10
Q

Write a balanced equation for the reaction catalyzed by a kinase for glycogen metabolism

A

2 ATP + Phosphorylase b –> 2 ADP + Phosphorylase A

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11
Q

What protein side chains are involved in this reaction that regulates glycogen metabolism?

A

Serine residues

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12
Q

What molecule serves as the phosphoryl donor

A

ATP

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13
Q

Write a balanced equation for the reaction catalyzed by a phosphatase

A

Phosphorylase A + 2H2O –> Phosphorylase B + 2Pi

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14
Q

Discuss how phosphate addition/removal causes conformational chances

A
  1. Phosphorylation has a lot of negative charges that interfere with interactions between substrates –> forces proteins into different conformations
  2. Phosphorylation Of an enzyme can also alter substrate-binding affinity via electrostatic repulsion
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15
Q

Discuss the epinephrine signal transduction pathway

A

*remember, epinephrine will be used when your body wants to engage in fight or flight
- Epinephrine will bind to the Beta-Adrenergic receptor
- Allosteric change in hormone complex causes the GDP bound to the alpha subunit to be replaced by a GTP activating the Alpha subunit.
- Activated alpha subunit separate from other subunits and moves towards adenylyl cyclase, activating it. Many alpha subunits may be activated by one receptor
- Adenylyl cyclase catalyzes the formation of cAMP using ATP
- Two cAMP molecules will activate PKA
- Phosphorylation of cellular proteins by PKA causes the cellular response to epinephrine

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16
Q

What are the target enzymes of PKA?

A

Glycogen phosphorylase and glycogen*

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17
Q

When glycogen phosphorylase and glycogen synthase are phosphorylated are they active or iinactive?

A
  • Glycogen phosphorylase: active
  • Glycogen synthase: inactive
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18
Q

Note: the bifunctional enzyme taht regulates the level of fructose 2,6 bisphosphate in the cell is also regulated via this cascade

A
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19
Q

Illustrate the principle of amplification within the signal transduction cascade. Point out each step that results in signal amplification

A

1 epinephrine can trigger possibly hundreds of G proteins, each which goes on to activate a molecule of adenylyl cyclase. Adenylyl cyclase produces many molecules of cAMP

Hepatocyte:
- G-alpha is amplified by epinephrine
- Adenylyl cyclase amplifies cAMP
- Active PKA amplifies active phosphorylase b
Active glycogen phosphorylase a amplifies glucose 1-phosphate which makes a whole lot of glucose

*Because two molecules of cAMP are requried to activate one PKA catalytic subunit, this steps doesnt amplify the signal!

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20
Q

How does the G protein inactivate

A
  • The G protein can inactivate due to GAPs and RGSs that will determine how long the G protein will remain active until its hydrolyzed
  • It can also inactivate by itself if epinephrine levels decrease enough
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21
Q

How is adenylyl cyclase inactivated?

A

With the inactivation of the G protein, specifically, G alpha

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22
Q

Name the enzyme that degrades residual cAMP in the cell

A

Cyclic nucleotide phosphodiesterase

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23
Q

How is PKA inactivated?

A

Low concentration of cAMP (due to cyclic nucleotide phosphodiesterase)

24
Q

How is the activity of the target enzymes reversed?

A

At the end of the signaling pathway, teh metabolic effects that result from phosphorylation of target enzymes by PKA are reversed by phospho[protein phosphatases, which hydrolyze the phosphorylates Tyr, Ser, or Thr residues releasing the inorganic phosphate

25
Q

How is the receptor protein desensitised?

A
  • Desensitization, damps teh response even as the signal persist in comparison to the other methods of signal termination (in those other methods, the signal was stopped)
  • G protein Beta and Gamma will recruit Bark to the membrane, where it phosphorylates Ser residues at the C terminus of the receptor
  • Beta-arrestin binds to the phosphorylated carboxyl-terminal domain of the receptor
  • Receptor-arrestin complex enters the cell by endocytosis
  • In endocytic vesicle, arrestin dissociates; receptor is dephosphorylated and returned to cell surface
26
Q

Fatty acids are stored in adipose cells as triacylglycerol. Draw the structure of triacylglycerol using R to represent the long chain fatty acid tail

A

*draw

27
Q

Discuss the activation of lipase in adipocytes through hormone sensitive amplification

A
  1. Glucagon binds to GPCR
  2. Adenylyl cyclase produced cAMP
  3. PKA phosphorylates HSL and perilipin (on the surface of the liquid droplet)
  4. Phosphorylation of perilipin causes CGI-58 to dissociate and recruit ATGL to the droplet surface
  5. Active ATLG converts triacylglycerol to diacylglycerol. The phosphorylated perilipin associates with the phosphorylated HSL allowing it (the HSL) to access the surface of the droplet
  6. HSL now that its at the surface of the droplet converts diacylglycerol to monoacylglycerol
  7. A third lipase, MGL hydrolyzes the monoacylglycerol
  8. All the three fatty acids that were created leave the adipocyte and are transported into the blood bound to serum albumin.
  9. They are released from the albumin and enter a myocyte via a fatty acid transporter.
28
Q

Using structures, write a balanced chemical equation for the reaction catalyzed by lipase

A
29
Q

How are the hydrophobic fatty acids stabilized in the blood as they are transported to tissues?

A

They bind to the blood protein serum albumin which makes them soluble

30
Q

What is the fate of the glycerol backbone?

A

The glycerol backbone will ultimately be converted into dihydroxyacetone phosphate which can be used in either glycolysis or gluconeogenesis

31
Q

Using structures, write a balanced chemical equation for the cytoplasmic reaction that results in activation of fatty acids. What aspect of the activation process drives the reaction to completion?

A

Fatty acid + ATP + CoASH –> Fatty acyl-CoA + AMP + 2Pi

32
Q

Where in the eukaryotic cell does fatty acid oxidation occur?

A

The Mitochondria Matrix

33
Q

Discuss how the activated fatty acid is carried into this membrane bound compartment

A
  • Carnitine acyltransferase 1 on the outer mitochondrial membrane will transiently swap out with the S-CoA to form fatty acyl carnitine
  • The fatty acyl carnitine then diffuses across the intermembrane space and enters the matrix through the acylcarnitine/carnitine cotransporter
  • Once inside the matrix, the fatty acyl group is transferred from the carnitine back to coenzyme A from the intramitochondrial by carnitine acyltransferase 2
34
Q

Discuss the three stages through which energy is derived from fatty acid degratation

A

1st stage: Beta oxidation
- Fatty acids undergo oxidative removal of successive 2-carbon units in the form of acetyl-CoA, starting from the carboxyl end of the fatty acid chain
2nd stage: TCA cycle
- The acetyl groups of acetyl CoA are oxidized to CO2 in the citric acid cycle
3rd stage: ETC
- The first two steps produce NADH and FADH2 which donate electrons to the mitochondrial respiratory chain, through which the electrons pass to oxygen with the concomitant phosphorylation of ADP–>ATP

35
Q

Show the details of a single round of Beta oxidation (Draw)

A

Draw

36
Q

Which reactions of the TCA cycle are similar to reactions in Beta-oxidation

A
  • First dehydrogenation step is similar to succinate converting into fumarate
  • The hydration step afterwards is similar
  • The second dehydration step mirrors malate to oxaloacetate
37
Q

Write the net reaction for the Beta-Oxidation of palmitoyl CoA

A

palmitoyl CoA + + 7CoA + 7FAD + 7NAD+ + 7H2O –> 8 acetyl CoA + 7FADH2 + 7NADH + 7H+

38
Q

Considering the P/O ratios for NADH and FADH2 that you learned in Unit 12, how many ATPs can be generated through subsequent oxidation of reduced flavin (FADH2) and pyridine (NADH) nucleotides

A

7 FADH2 (1.5)
7 NADH (2.5)
= 28 ATP

39
Q

The acetyl CoA now enters the citric acid cycle.. How many ATPs can be made from the oxidation of acetyl CoA?

A

Citric acid cycle produces: 1 FADH, 3 NADH, and 1 ATP

Since we have 8 acetyl-CoA
8 FADH (1.5)
24 NADH (2.5)
8 ATP

Total is 80 ATPs

40
Q

What is the total yield of ATP formed during oxidation of one molecule of Palmitoyl CoA

A

108 ATPs

41
Q

Give at least two examples of the fact that synthetic and degradative pathways are not simply reversals of one another

Why is this fact important in biological systems?

A
  1. Fatty acid synthesis/degradation
  2. Glycolysis and gluconeogenesis

Synthetic pathways often require energy so reversing a pathway for degradation may not be energetically favorable or efficient

42
Q

What is the rate limiting step in fatty acid biosynthesis?

A

The formation of malonyl CoA from acetyl CoA

43
Q

Write, with structures, the reaction which represents the activation of acetyl CoA for biosynthesis

A

Draw

44
Q

Name the enzyme that catalyzes the conversion of acetyl CoA to malonyl CoA

A

Acetyl CoA carboxylase

45
Q

What are the steps for fatty acid synthesis?

A

Condensation
Reduction
Dehydration
Reduction

46
Q

Draw out how fatty acid synthesis occurs

A
47
Q

HCO3- is an important player in fatty acid biosynthesis. Does the carbon from HCO3- become incorporated into the fatty acid backbone?

A

No, it doesn’t. It is released as CO2 during the first condensation phase as the two carbon unit is added

48
Q

Why do cells go to the trouble of adding CO2 to make a malonyl group from the acetyl group, only to lose CO2 again during the formation of fatty acids

A

The use of activated malonyl groups rather than acetyl groups makes the condensation reaction thermodynamically favorable. Coupling the condensation to the decarboxylation of the malonyl group renders the overall process highly exergonic

49
Q

Write a balanced chemical equaton for a similar carboxylation/decarboxylation sequence in gluconeogenesis

A

Pyruvate + HCO3- + ATP + GTP –> PEP + GDP + CO2 + ADP + Pi

50
Q

Compare the steps for fatty acid degradation and fatty acid synthesis

A

Degradation:
- Reduction
- Hydration
- Reduction
- Thiolysis

Synthesis:
- Condensation
- Reduction
- Dehydration
- Reduction

51
Q

An important generalization in metabolism is that NADH is generated in degradative reactions and NADPH is utilized in biosynthetic reactions. Does this generalization hold true for fatty acid degradation and synthesis

A
  • Yes

Remember that in synthesis its NADPH turning into NADIP+

52
Q

In general, degradative pathways generate ATP and biosynthetic pathways consume ATP. In which steps in fatty acid synthesis is ATP utilized?

A

In the converting of HCO3- to CO2

53
Q

How many molecules of malonyl CoA are required to synthesize a 16 carbon fatty acid chain?

A

7 malonyl CoA

54
Q

How many NADPHs are required for the synthesis

A

14 NADPH’s

55
Q

Write a balanced equation for the net reaction for palmitate synthesis from acetyl CoA.

A

Acetyl-CoA + 7 malonyl CoA + 14 NADPH + 14H+ –> Palmitate + 14 NADP+ + 7CO2 + 8CoA + 6H20

56
Q
A

Biochem (15 decks)

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