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Biochem > Unit 13 (2) > Flashcards

Unit 13 (2) 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 and liver
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2
Q

Using structures, write the reaction catalyzed by glycogen phosphorylase. What is the result of this step?

A

DRAW
- Glucose 1 phosphate

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3
Q

What is the enzyme used to break down glycogen into free glucose?

A
  • It’s glycogen phosphorylase. It causes a inorganic phosphate to attack the glycogen chain on the nonreducing end.
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4
Q

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

A

The product of glycogen phosphorylation is glucose 1 phosphate. This can be converted into glucose 6 phosphate which can be used in glycolysis. This is energetically favorable because we were able to add a phosphate to glucose without using ATP (which is costly). If we were to do hydrolysis, we wouldn’t have this product

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5
Q

List several reasons why sugar nucleotides are suitable for biosynthetic reactions

A
  1. Formation of the sugar nucleotide is irreversible because a pyrophosphate is released and this will be broken down into Pi which drives the reaction forward by Le Chatelier’s
  2. Nucleotides contribute to the delta G of enzymatic reactions by engaging in noncovalent interactions with the active site.
  3. Nucleotide is a good leaving group
  4. To separate out (tag) hexoses (sugars) that are meant to be for storage and those that are for other processes
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6
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
Glucose + ATP –> Glucose 6 Phospahate
Glucose 6 P –> Glucose 1 P

Glucose 1 P + UTP –> Glucose UDP
The other product of this reaction is pyrophosphate. This is important because it will be broken down into 2 Pi which is drive the reaction forward and essentially make it irreversible

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7
Q

Using structures, write the balanced equation for the reaction catalyzed by glycogen synthase (you don’t have to draw this)

A

Glucose UDP + glycogen –> elongated glycogen

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8
Q

What is the enzyme that lengthens the glycogen?

A

Glycogen synthase

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9
Q

Discuss the biological significance of the branched structure in glycogen

A
  • Branching increases the number of nonreducing ends, meaning there are more sites to add to the glycogen polymer and more sites to break it off
  • Branching also makes the polymer more soluble
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10
Q

Which enzyme benefits from having more reducing ends?

A

Both! Trick question

Glycogen phosphorylase can only use its Pi to attack at the nonreducing end

Glycogen synthase can only have the glycogen polymer add with the nonreducing end

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11
Q

Write a balanced equation for the reaction catalyzed by glycogen phosphorylase b kinase

A

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

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12
Q

What protein side chains are impacted in the addition of phosphates on phosphorylase b kinase

A

Serine residues

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13
Q

What molecule serves as the phosphoryl donor?

A

ATP

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14
Q

Write the balanced equation for the reaction catalyzed by glycogen phosphatase

A

Phosphorylase a + 2H2O => Phosphorylase b + 2Pi

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15
Q

Discuss how the addition/removal causes conformational changes that alter enzyme activity

A

1) Phosphate groups are very bulky and negatively charged so they can force proteins into different conformations due to their charge
2) Can also interfere with substrate binding due to electrostatic repulsion

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16
Q

Draw out and discuss the epinephrine pathway. Discuss the logic behind it

A
  • Epipnephrien is a signal of distress. We will want more sugar available when we have this signal
  • Epinephrine will bind to a Beta adrenergic receptor
  • This induces a conformational change in the receptor. The receptor also happens to be a GPCR. The change in confromation allows for the G-alpha subunit to release its GDP and gain a GTP
  • The activated G-alpha subunit will then leave the beta and gamma subunits to activate adenylyl cylcase
  • Activated adenylyl cyclase will take ATP and use that to make cAMP and PPi (which makes this step drive forward)
  • Two cAMPs are needed to activate one PKA molecule. When activated, PKA can phosphorylate many target enzymes

Three important targets:
- glycogen phosphorylase b kinase
- PFK 2
- glycogen synthase

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17
Q

What are the three important targets of PKA? What happens to them when they are phosphorylated?

A

Three important targets:
- glycogen phosphorylase b kinase
- PFK 2
- glycogen synthase

Glycogen phosphorylase b kinsae will be activated and can add 2 ATPs to phosphorylase b so it can become active (phosphorylase a) and can cause the breakdown of glycogen

PFK 2 is inactive when phosphorylated while FBPase 2 is activated when phosphorylated. The inactivation of PFK 2 encourages Fructose 2,6 bisphosphate to turn into Fructose 6 bisphosphate and calls for gluconeogenesis

Glycogen synthase is inactivated when phosphorylated. This makes sense because we don’t want to keep making glycogen if we need to use it

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18
Q

Note that the level of fructose 2,6 bisphosphate is regulated, explain how

A

When the PFK2/FBPase is phosphorylated, PFK2 is inactive and FBPase is active. In this case, fructose 2,6 BP is not generated so it cant increase PFK1 and increase glycolysis

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19
Q

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

A
  • All steps will amplify the signal except for cAMP to PKA. The reason why is because you only need two cAMP molecules to activate PKA
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20
Q

How does the G protein inactivaate?

A

1) There are GAPs and RGSs that will hydrolyze teh GTP on the G-alpha subunit
2) The G-alpha subunit will eventually hydrolyze its GTP on its own

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21
Q

How is adenylyl cyclase inactivated?

A

When the G protein inactivates, G-alpha specifically, adenylyl cyclase is inactivated as well

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22
Q

Name the enzyme that degrades the residual cAMP in the cell

A

Cyclic nucleotide phosphodiesterase

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23
Q

How is PKA inactivated?

A

Low levels of cAMP due to cyclic nucleotide phosphodiesterase

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24
Q

How is the activity of the target enzymes reversed?

A
  • There are always protein phosphatases present; however, when PKA is activated, it outcompetes them and phosphorylates its target proteins. However, when PKA levels are low, the phosphatases can come and remove the phosphates that were added
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25
Q

How is the receptor protein desensitized?

A
  • There are times where the signal is still present and the receptor wants to be desensitized to it.
  • The gamma and beta subunits of the GPCR will recruit BARK.
  • Bark will phosphorylate the Ser residues on the C terminus of the Beta adrenergic receptor
  • This will recruit Beta-arrestin which will cause the receptor to be endocytosed into the cell. Once endocytosed, it will be dephosphorylated and returned to the surface. Beta arrestin also leaves
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26
Q

Where are fatty acids stored?

A

In adipose cells which are in fatty tissues.

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27
Q

Draw the structure of a triacylglycerol using R to represent the long chain fatty acid tail

A
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28
Q

Draw the structure of glycerol

A
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29
Q

Explain how glucagon can start the pathway that will create fatty acids. Explain how the fatty acids are created

A
  • Glucagon is a signal that there are low levels of sugar in the cell. It will bind to a receptor on an adipose cell
  • The receptor is a GPCR, will activate adenylyl cyclase which produces cAMP, and PKA is activated
  • PKA will phosphorylate HSL, a type of lipase and perilipin.
  • The activated perilipin will bring the HSL to the surface of the lipid droplet so the HSL can convert the triacylglycerol into 1 glycerol and 3 fatty acids
  • The fatty acids will then bind to the protein, serum albumin, so it can be soluble in the blood, and will be transported to its target cell so it can enter the cytosol
30
Q

Write a balanced equation for the reaction catalyzed by lipase

A

Triacylglycerol + H2O –> Glycerol + 3 Fatty acids

31
Q

What is the role of a lipase?

A

To hydrolyze the triacylglycerols into fatty acids

32
Q

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

A

They bind to serum albumin, the protein

33
Q

What is the fate of the glycerol backbone?

A
  • The glycerol backbone will:

glycerol –> glycerol 3 phosphate –> dihydroxyacetone phosphate –> glyceraldehyde 3 phosphate

  • phosphate is added to glycerol
    Can enter glycolysis or gluconeogenesis depending on what the cell needs at that time
34
Q

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

*draw and explain why this happens

A
  • Once the fatty acid has been transported into the cytosol, it needs to enter the mitochondrial matrix to undergo Beta-oxidation, to do this it must be transformed
  • Fatty acid + ATP + CoASH –> Fatty Acyl-CoA + 2Pi + AMP
  • The PPi that is released will turn into Pi which drives this reaction forward
    *AMP
35
Q

Where in the eukaryotic cell does fatty acid oxidation occur?

A

In the mitochondrial matrix

36
Q

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

A
  • Fatty acyl-CoA is impermeable to the membrane
    -Carnitine acyl transferase 1 will swap the CoA group for a carnitine so the molecule can now pass the acylcarnitine/carnitine transporter
  • Once it enters the mitochondrial matrix, a carnitine acyltransferase 2 will swap the carnitine group for a CoA again
37
Q

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

A
  • From Beta-oxidation alone, we generate 1 FADH2, 1 NADH, and 2 Acetyl-CoAs
  • In the TCA cycle, these 2 Acetyl-CoAs could go to individually make 1 FADH2, 3 NADH, and 1 ATP
  • Lastly, in the ETC, the electron carriers from these steps will drive the movement of 10H+ if its NADH and 6H+ if its FADH2. This will ultimately make 2.5 ATP per NADH and 1.5 ATP per FADH2
38
Q

Discuss and draw the steps for a single round of Beta-oxidation. Draw it for palmitoyl-CoA

A

Steps:
- Dehydration (FAD–> FADH2)
- Hydration (add H2O) *furthest carbon from SCoA
- Dehydration (NAD+ –> NADH)
- Thiolysis

39
Q

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

A

Steps:
- Dehydration (FAD–> FADH2)
Similar to:
Succinate –> fumarate

  • Hydration (add H2O)
    Similar to:
    Fumarate to malate
  • Dehydration (NAD+ –> NADH)
    Similar to:
    Malate to Oxaloacetate
40
Q

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

A

Palmitoyl-CoA + 7FAD + 7H2O + 7NAD+ + 7CoAs –> 8 Acetyl CoAs + 7FADH2 + 7NADH + 7H+

41
Q

Considering the P/O ratios, how many ATP are you generating from beta-oxidation alone and from the 8 acetyl-CoA in beta-oxidation entering the TCA cycle? What is the overall ATP yield?

A
  • Be careful to know that one round of TCA will create 1 FADH2, 3 NADH, and 1 ATP (this isn’t doubled like how pyruvate is because in pyruvate, there are two molecules)

108 ATPs

42
Q

Where does fatty acid synthesis occur? Where does fatty acid degradation occur?

A

in the cytosol
in the mitochondrial matrix

43
Q

Is NADPH an oxidant or reductant?

A

It is used as a reductant for many biosynthetic processes

44
Q

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

A
  1. Fatty acid synthesis and degradation
  2. Glycolysis and gluconeogenesis
45
Q

Why is it important that synthetic and degradative pathways aren’t just the reversal of one another?

A

Many of these pathways release high amounts of energy, so it would be impossible to reverse. This is important because it helps us with regualtion

46
Q

What is the rate limiting step in fatty acid synthesis?

A

The formation of malonyl CoA

47
Q

Write, with structures, the reaction which represents the activation of acetyl CoA. Name the enzyme that catalyzes the conversion of acetyl CoA into malonyl CoA

A
  • Acetyl CoA carboxylase
48
Q

Which prosthetic group is involved in teh activation of acetyl CoA for fatty acid synthesis? Discuss its role.

What compound is required before the carboxyl group from HCO3- can be transferred to the biotin

A
  • Biotin. It carries the carboxyl group from one site to the other. The second site contains the acetyl-CoA
  • ATP
49
Q

Draw out the four step sequence that lengthens a growing fatty acyl chain by two carbons

A

Condensation
Reduction
Dehydration
Reduction

50
Q

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

A

No, its removed essentially in the first step, right after it is added

51
Q

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

A

The reason why we form a malonyl CoA is so that when we do the condensation reaction (that is unfavorable) we have that CO2 group on our malonyl CoA that will spontaneously undergo decarboxylation which is favorable

52
Q

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

A

Pyruvate + HCO3- + ATP –> Oxaloacetate + ADP + Pi

Oxaloacetate + GTP –> GDP + PEP + CO2

53
Q

How does the series of reactions in fatty acid synthesis compare to fatty acid degradation

A

Synthesis:
Condensation
Reduction
Dehydration
Reduction

Degradation:
Dehydrogenation
Hydration
Dehydrogenation
Thiolysis

54
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, emphasis on the NADPH is USED to donate electrons in this case instead of gaining them

55
Q

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

A

ATP converts HCO2- to CO2

56
Q

What is the net equation for fatty acid synthesis of palmitate

A

Acetyl-CoA+ 7 malonyl-CoA + 14 NADPH + 14H+ –> palmitate + 7CO2 + 8CoA + 14NADP+ + 6H2O

57
Q

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

A

7 malonyl CoA

58
Q

How many NADPH are required for the synthesis of the palmitate

A

14 NADPH

59
Q

Write a balanced equation for the net reaction for palmitate synthesis from acetyl CoA. There are only 6 waters because one is used to cleave the fatty acid from the enzyme

A

8 Acetyl CoA + 7ATP + 14 NADH + 14H+ –> palmitate + 8 CoA + 7ADP + 7Pi + 14NADP+ + 6H2O

60
Q

Draw palmitate

A

H3C - CH2 - CH2 - CH2 … -CH2- COO

61
Q

What two- or three carbon compound gives rise to each numbered section shown in palmitate molecule

A

Group one is from acetyl-CoA, the other groups (2-8) are from malonyl CoA

62
Q

Do question D on page 63

A
63
Q

Describe how acetyl CoA is translocated from the inside of the mitochondrion to the cytosol and how NADPH can be generated in the process

THink about this because there’s something you said wrong the first time

A

Acetyl CoA react with oxaloacetate to form citrate. Citrate can leave the matrix and enter the cytosol. The citrate will convert back into acetyl CoA and Oxaloacetate, but now the Oxaloacetate must get back into the matrix. The oxaloacetate will turn into malate (using NaDH–> NAD+).

*The malate will convert into pyruvate, using NADP+ to create NADPH. It also loses a CO2 in this process

64
Q

How many NADPH are needed to synthesize one molecule of palmitate

A

14 NADPH

65
Q

How many NADPH can be generated as a result of the shuttling of acetyl CoA

A

1 NADPH

66
Q

Does the NADPH generated in this cycle suffice for fatty acid synthesis? If not, from which pathway does the remainder come?

A

The pentose-phosphate pathway
* 2NADPH per cycle

67
Q

What enzyme in fatty acid synthesis is the rate-limiting step and is therefore an important part of regulation?

A

Acetyl-CoA carboxylase

68
Q

In vertebrates, what compound acts as an allosteric feedback inhibitor? What compound is an allosteric?

Draw the diagram

A
  • Activator is citrate
  • Inhibitor is palmitoyl-CoA
69
Q

Discuss how this enzyme is also regulated by hormone-regulated covalent modifications

A
  • Glucagon and epinephrine will phosphorylate acetyl-CoA carboxylase, inactivating it

High levels of AMP can also do this

70
Q

Discuss the role of F 2,6 BP accumulation in allowing excess carbohydrates to be converted to fat.

A

We only want carbohydrates to be converted into fat when we have a high amount of blood sugar.

Insulin will dephosphorylate PFK2 to activate F 2,6 BP

F 2,6 BP will activate glycolysis which will lead to an upsurge of ATP and citrate. These will begin to inhibit the glycolysis

However, F 2,6 BP is still stronger than this inhibition if it continues to get signals from insulin. The high levels of ATP and Citrate allow for high levels of ATP and Acetyl-CoA

When we have high levels of ATP and Acetyl-CoA, the citrate can leave the matrix and allosterically active the acetyl-CoA carboxylase, allowing for fatty acid synthesis

71
Q

How is futile cycling avoided in fatty acid synthesis?

A
  • Malonyl CoA inhibits carnitine acyltransferase I, effectively stopping glycolysis

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