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Biochemistry 450 > Final > Flashcards

Final Flashcards

1
Q

Glycolysis Reaction #5:
What is the product?
What is the enzyme that catalyzes it and why is it unique?
What intermediate is produced?

A
  • GAP is converted into G3P (glyceraldehyde 3-phosphate).
  • Enzyme is triose phosphate isomerase, which is a perfect enzyme to prevent accumulation of toxic intermediate: enediol.
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2
Q

What is Delta G zero prime of glycolysis reaction #5? What does everything after this step have?

A

Delta G zero prime is close to zero, so reaction is readily reversible.
Everything after this step has 2 molecules.

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3
Q

Glycolysis Reaction #6:
What products are formed?
What is special about this step?
What enzyme is used?

A

Glyceraldehyde 3-phosphate and NAD+ is converted to 1,3 Bisphosphoglycerate (1,3 BPG) and NADH.
This is the only oxidation in glycolysis.
It is catalyzed by glyceraldehyde-3-phosphate dehydrogenase.

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4
Q

Glycolysis Reaction #6:

What provides energy and how does reaction take place?

A

Oxidation of NAD+ is used as energy to put phosphate on reactant to make it 1,3-BPG which has higher energy than ATP.

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5
Q

Glycolysis Reaction #7:
Describe Reaction- How do?what products form?
What enzyme is used?

A
  • High energy 1,3-BPG uses its energy to transfer phosphate to ADP and make it ATP. (Now have 2 molecules of ATP)
  • Forms ATP and 3PG (3 phosphoglycerate)
  • Enzyme: Phosphoglycerate Kinase-adds phosphate to ADP
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6
Q

Glycolysis Reaction #8:
Reactant and products?
Enzyme?
Intermediate? What is it used for?

A

Converts 3PG to 2PG.
Catalyzed by phosphoglycerate mutase
Makes 2,3 BPG intermediate released in low rate. Switches hemoglobin to T state when bound to it.

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7
Q

Glycolysis Reaction #8:

Why does 2,3 BPG form?

A

Because reaction #8 is not like isomerases. The enzyme puts phosphate on carbon 2 first and leave carbon 3 alone. Making 2,3 BPG. Then it clips phosphate off carbon 3 later on, making the product 2PG.

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8
Q

Glycolysis Reaction #9:
Reactants and products:
Enzyme:
What does the enzyme do and what is unique about the product?

A

2PG converted to PEP (phosphoenolpyruvate) by enzyme enolase.
Enolase removes water from 2PG to form a double bond high energy product (PEP).

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9
Q

Glycolysis Reaction #10:
What does the overall reaction entail?
Reactant and products?
Enzyme?

A

Substrate level phosphorylation to make ATP.
PEP converted to pyruvate by adding phosphate to ADP and making ATP. (almost enough e to make 2 ATPs)
Enzyme is pyruvate kinase.

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10
Q

Glycolysis Reaction #10:

Describe the delta G zero prime and its effects.

A

Delta G zero prime is highly negative and pulls all reactions before it forward.

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11
Q

Glycolysis Reaction #10:

What inactivates/activates pyruvate kinase?

A

It is allosterically inactivated by ATP and allosterically activated by F1,6BP.
Also inactivated by phosphorylation seen in glycogen metabolism.

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12
Q

What is the activation of pyruvate kinase (from reaction 10) by F 1,6BP (from reactions 3 and 4) an example of?

A

Example of “feed forward”, as more F16BP means more production of ATP/ pulling glycolysis reaction forward.

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13
Q

Examples of high energy enzymes:

A

Hexokinase, PFK, Aldolase, Pyruvate Kinase

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14
Q

What does redox balancing relate to? Why is it important?

A

Important for glycolysis (especially reaction 6 which is sensitive to NAD+/NADH ratio). Relates to relative amounts of NAD+ and NADH in cell.

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15
Q

What is the fate of pyruvate in an aerobic cell if there is plenty of NADH+ and oxygen present?

A

Converts pyruvate to acetyl-CoA for oxidation in citric acid cycle.

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16
Q

What is fate of pyruvate in a animal cell if oxygen is absent (making the NAD+ levels go naturally down because electron transport chain can’t convert NADH to NAD+)

A

Pyruvate is converted to lactate which requires NADH and produces NAD+.

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17
Q

What is fate of pyruvate in a bacterial/yeast cell if oxygen is absent (making the NAD+ levels go naturally down because electron transport chain can’t convert NADH to NAD+)

A

Pyruvate is converted to ethanol which requires NADH and produces NAD+. (fermentation)

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18
Q

What is the difference between anaerobic conversion and aerobic conversion of NADH to NAD+?

A

Anaerobic (absence of oxygen) metabolism generates only 2 ATPs per glucose while Aerobic metabolism generates 38 ATPs per glucose.

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19
Q

How can sugars other than glucose be metabolized by glycolysis?

A

If they are converted to intermediates of glycolysis.

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20
Q

How can fructose enter the glycolysis pathway?

A

It can be converted to fructose 6-phosphate by hexokinase or converted to fructose 1-phosphate (F1P) by fructokinase.
F1P can be converted to glyceraldehyde and DHAP without PFK. Forces pyruvate production.

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21
Q

What is thought to be caused by ingestion of a lot of fructose?

A

Obesity

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22
Q

How can galactose enter the glycolysis pathway?

A

Galactose converted to galactose 1-phosphate (by galactokinase) and then to glucose 1-phosphate by swapping sugars with UDP glucose. Then is made into glucose 6-phosphate.

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23
Q

what does deficiency of galactose enzymes result in? What enzyme is involved?

A

Results in accumulation of galactose (from break down of lactose) which is then converted into galactitol by enzyme aldose reductase.

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24
Q

What does galactitol cause?

A

Galactitol accumulation in the human eye lens causes it to absorb water and may cause cataracts.

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25
Q

Where do all glycolysis reactions occur?

A

In the cytoplasm

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26
Q

Where do all gluconeogenesis steps occur?

A

All but 2 of the steps occur in cytoplasm.
The first step to form oxaloacetate from pyruvate occurs in the mitochondria.
The last step to make G6P into glucose occurs in the ER lumen.

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27
Q

What does the deficiency of enzyme lactase lead to?

A

Lactose intolerance.

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28
Q

3 enzymes important to regulation of glycolysis:

A

Hexokinase, PFK, and pyruvate kinase

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29
Q

Why is Hexokinase’s regulation important to glycolysis?

A

Its regulation is complicated by it is dependent on accumulation of products (G6P).

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30
Q

Why is PFK’s (which is thought to be most important enzyme) regulation important to glycolysis?

A

It has an allosteric binding site for ATP (which inactivates it) and substrate binding site. Km for allosteric binding site is higher so active site has greater affinitiy.

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31
Q

Describe the role of F2,6BP is PFK regulation in glycolysis and F1,6BPase regulation in gluconeogenesis

A

F2,6BP (which is NOT an intermediate of glycolysis) strongly activates PFK at low concentrations.
It inhibites F1,6BPase of gluconeogenesis.

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32
Q

Why is pyruvate kinase regulation important to glycolysis?

A

Pyruvate kinase is regulated by allostery and covalent modification. Turned off by ATP and alanine (easily made from pyruvate). Turned on by F16BP (“feed forward” activation). Phosphorylated by protein kinase turns off.

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33
Q

Hypoxia:

A

Cells that are short of oxygen

34
Q

How do cells respond to hypoxia?

A

activating Hypoxia Induction Factor 1 (HIP-1) which is a transcription factor that activates transcription of genes involved in glucose transport and glycolysis.

35
Q

What type of cells are usually hypoxic and induce HIF-1? How else do they battle hypoxia? (What other factor do they make?)

A

Cancer cells are hypoxic. They also stimulate growth of blood vessels to them by making another factor called angiogenin.

36
Q

Two cancer therapies:

A

Blocking HIF-1 and angiogenin.

37
Q

Gluconeogenesis:

where does it occur?

A

reverse of glycolysis. Synthesis of glucose from pyruvate. Occurs in liver and part of the kidney.

38
Q

How does gluconeogenesis overcome energetically unfavorable reactions?

A

It uses four enzymes to replace 3 energetically unfavorable reactions in glycolysis.

39
Q

What are the 3 energy barriers that must by overcome during gluconeogenesis.

A

1) Pyruvate Carboxylase (mitochondria) and PEP carboxykinase (PEPCK in cytoplasm) are used instead of pyruvate kinase of glycolysis.
2) F16BPase is used instead of Phosphofructokinase (PFK) of glycolysis to make F16BP to F6P.
3) Glucose 6-phosphatase (G6Pase) is used instead of hexokinase of glycolysis to make glucose.

40
Q

How are Pyruvate carboxylase and PEPCK used instead of pyruvate kinase in gluconeogenesis? What are the energy sources?

A

Pyruvate Carboxylase takes ATP and bicarbonate (CO2) source to make the 4 carbon compound oxaloacetate, which is then converted to PEP used PEPCK and GTP energy.

41
Q

What mechanism do F16Pase and G6Pase enzymes of gluconeogenesis use?

A

They use similar mechanisms, clip off a phosphate from their substrate, thus avoids synthesis of ATP (would be required if glycolysis was just reversed)

42
Q

How is a carboxyl group added to pyruvate to make oxaloacetate in gluconeogenesis?

A

The carboxyl group is added using a coenzyme of pyruvate carboxylase called Biotin, which carries carbon dioxide for attachment.

43
Q

Which sugar metabolism pathway do high cellular energy molecules (ATP) favor?

A

Favor gluconeogenesis and inhibit glycolysis.

44
Q

Which sugar metabolism pathway do low energy molecules (ADP or AMP) favor?

A

Favor glycolysis and inhibit gluconeogenesis.

45
Q

Reciprocal Regulation:

What is an example?

A

When the same compound/same action has the opposite effects on a anabolic (gluconeogenesis) and catabolic (glycolysis) reactions.
Ex: either making or breaking down F2,6BP having opposite effects on glycolysis and gluconeogenesis.

46
Q

Futile cycle
Why is it bad?
What does stops it?

A

When catabolic and anabolic reactions occur simultaneously. This is a waste of energy by the cell and is stopped by reciprocal regulation.

47
Q

What is so unique about how F2,6BP is made/degraded?

A

F2,6BP is made and degraded on two difference portions of the same protein.

  • Portion PFK2 is kinase portion and catalyzes synthesis of F26BP from F6P.
  • Portion FBPase-2 is the phosphatase portion and catalyzes breakdown of F26BP.
48
Q

How does binding of epinephrine affect the reciprocal regulation?

A

Epinephrine binding to 7TM andrenergic receptor causes Protein Kinase A to phosphorylate the protein and causes inactivation of PFK2 and activation of FBPase-2.
-This means that F26BP will be broken down and gluconeogenesis is favored while glycolysis is not.

49
Q

How does binding of insulin affect the reciprocal regulation?

A

Binding of insulin to a cell receptor causes phosphoprotein phosphatase to dephosphorylate the protein and causes the activation of PFK2 and inactivation of FBPase-2.
-This means that F26BP will be made and glycolysis will be favored while gluconeogenesis will not.

50
Q

How is F26BP made?

A

Starts with F6P and ATP and uses Phosphofructokinase-2 to make F26BP. (as opposed to Phosphofructokinase 1 used to make F16BP).

51
Q

What is the Cori cycle and what induces it?

A

Provides glucose for muscles that is made in the liver.

Occurs when exercise occurring faster than oxygen is being delivered to muscles.

52
Q

Describe the steps of the cori cycle:

A

1) Muscles convert glucose to pyruvate and then convert pyruvate to lactate in order to recreate NAD+.
2) Lactate is exported to bloodstream and then liver.
3) Liver reoxidizes lactate to make it pyruvate, and then makes it into glucose via gluconeoenesis.
4) glucose is taken back to bloodstream and muscles.

53
Q

Glycogen in animals:

what does branching allow

A

consists of alpha 1-4 linked glucose units with alpha 1-6 linkages at branch point (which occurs about every 10 units). Greater branching = greater ends to release glucose 1 phosphate (G1P).

54
Q

Amylose and Amylopectin in plants:

A

Amylose is unbranched and amylopectin is less branched.

55
Q

Where is glycogen stored in animals?

A

In liver and muscle tissues.

56
Q

How is G1P released from glycogen converted into G6P?

Describe delta G of this reaction.

A

Converted readily using enzyme phosphoglucomutase and G1,6BP is the intermediate.
Delta G zero prime is near zero, readily reversible and depends on substrate concentrations.

57
Q

What are the three fates of G6P?

A

1) In the muscle and brain (and most other tissues) G6P enters glycolysis and made into pyruvate/ATP.
2) In liver only G6P enters glucogenesis and makes glucose for bloodstream.
3) In other tissues G6P enters pentose phosphate pathway and is oxidized to produce NADPH and ribose.

58
Q

What is the enzyme responsible for breakdown of alpha 1-4 links of glycogen? Which links will it break down specifically?

A

Glycogen Phosphorylase. It will only catalyze phosphorylysis of glycogen units that are 4 residues and farther from a branch point (1-6 linkage).

59
Q

What mechanism does Glycogen Phosphorylase use to break down glycogen?

A

Uses phosphorylsis instead of hydrolysis, which means that it uses high energy from the 1,4 bond to add a phosphate to the glucose to form G1P instead of using ATP and hydrolysis to do it.

60
Q

What enzyme breaks down alpha 1,4 links close to branch points and alpha 1-6 links in glycogen?

A

Debranching enzyme, which removes 3 of the remaining 3 glucose units from a branch point, places them on a different branch using 1,4 links. It then removes the 1,6 link of the last glucose at branch point by hydrolysis.

61
Q

Describe the 4 states of glycogen phosphorylase:

A

1) Glycogen Phosphorylase A (GPa) in the T state
2) Glycogen Phosphorylase B (GPb) in the T state
3) Glycogen Phosphorylase A (GPa) in the R state
4) Glycogen Phosphorylase B (GPb) in the R state

62
Q

How is glycogen phosphorylase covalently modified?

A

When it is phosphorylated, it is referred to as GPa and when it is dephosphorylated it is called GPb.

63
Q

What phosphorylated glycogen phosphorylase b (GPb) to make it GPa?

A

Catalyzed by phosphorylase kinase enzyme which requires both calcium and phosphorylation by protein kinase A to be fully activated.

64
Q

How is GPb allosterically regulated?

A

-GPb is converted to the R state by AMP and converted to the T state by ATP and G6P. ATP and G6P are more abundant so GPb is usually in the T state.

65
Q

How is GPa allosterically regulated?

A

-GPa is converted to the R state randomly/automatically, and it is converted to the T state is glucose it present. (Glucose is rare so GPa is thought to favor the R state or be more active form)

66
Q

Phosphorylase kinase has an active and inactive form. What is the slow way to activate phosphorylase kinase (the enzyme that phosphorylates GPb to make GPa)

A

Needs calcium and protein kinase A to be active.
1) Slow Path: Epinephrine pathway stimulates protein kinase A to phosphorylate phophorylase kinase and partially activate it. Then calcium is added to fully activate it.

67
Q

What is the faster way to activate phosphorylase kinase

A

2) Fast Path: Calcium is added to the inactive form more instantaneously to partially activate phosphorylase kinase. Meanwhile epinephrine pathway has stimulated phosphorylation by activating protein kinase A.

68
Q

Epinephrine receptor Pathway (9 steps)

-Give first 5:

A

1) Epinephrine binds receptor
2) Receptor activates a G protein to bind GTP
3) Alpha subunit of G protein activates adenylate cyclase
4) Adenylase cyclase catalyzes formation of cAMP
5) cAMP activates protein kinase A

69
Q

Epinephrine receptor Pathway (9 steps)

-Give last 4:

A

6) Protein kinase A phosphorylates phosphorylase kinase, activates it.
7) phosphorylase kinase phosphorylates GPb to GPa
8) GPa breaks down glycogen to yield G1P.
9) G1P to G6P for glycolysis or gluconeogenesis.

70
Q

Overall, how is the synthesis of glycogen different from just a reversal reaction of glycogen breakdown?

A

An energy barrier must be overcome when synthesizing the alpha 1,4bond, which is accomplished by a “side-step” reaction that creates UDP-glucose (or UDPG) from G1P.

71
Q

What is the UDP-glucose synthesis reaction?

What pulls the reaction forward to UDPG direction?

A

Synthesis of UDP-glucose is done in the following reaction: UTP + G1P = UDPG + pyrophosphate (PPi).
-PPi is easily broken down, and reducing amount of it pulls reaction forward.

72
Q

What main enzyme is responsible for glycogen synthesis?

What are its two states?

A

Glycogen synthase:

1) Glycogen Synthase A (GSa): Not phosphorylated/Active
2) Glycoge Synthase B (GSb): phosphorylated/least active

73
Q

What effect does epinephrine (or its similar protein- glucagon) have of GP and GS? What is this an example of?

A

Binding of epinephrine ultimately results in phosphorylation of GPb and GSa to make GPa (more active) and GSb (less active). This causes release of G1P and more production of glucose, inhibition of glycogen synthesis -reciprical regulation.

74
Q

What effect does insulin have on GS?

A

Binding of insulin causes phosphoprotein phosphotase (PP1) to be active, which removes phosphates from all proteins. GSb (inactive) is dephosphorylated to make GSa (active). Glycogen synthesis is activated.

75
Q

What effect does insulin have on GP?

A

Binding of insulin causes GPa (active/phosphorylated) to be made into GPb (inactive/not phosphorylated). PP1 removes phosphate from glycogen phosphorylase kinase, which stops it from phosphorylating GP enzymes.

76
Q

What effect does epinephrine binding have on PP1?

A

Epinephrine activates protein kinase A phosphorylation and inactivates the enzyme PP1.

77
Q

How does epinephrine binding and protein kinase A activation inactive PP1?

A

PP1 binds to Gm/GL protein. Activation of protein kinase A causes Gm/GL to be phosphorylated, which causes PP1 to be released in a less active form. PKA also phosphorylates the PP1 inhibitor so it can bind to PP1 and totally inactivate it.

78
Q

Where is GP when PP1 is bound to Gm/Gl proteins?

A

PP1 is held close to GP when it is bound to Gm/Gl because this allows PP1 easy access to dephosphorylate GP and turn it off.

79
Q

What acts as a glucose sensor in liver cells?

A

GPa bound to PP-1/GL tightly, because if glucose is present it would switch to the inactive T state.

80
Q

When PP1 is bound to GPa is it active or inactive? What causes it to switch activity?

A

PP1 is inactive if the GPa is in the R state. If [glucose] increases, GPa flips to T state, and PP1/Gl complex is released from GPa and PP1 is active.

81
Q

What happens when PP1 is no longer bound to GPa?

What does this tell you about the reciprocal regulation of glycogen synthesis/ breakdown?

A

Release makes PP1 dephosphorylate GPa to make it GPb, and dephosphorylate GSb to make GSa.
-This tells you that glycogen breakdown is first stopped before glycogen synthesis is activated.

82
Q

What would happen when glucose, GPa, GSb, and glycogen are all present in a mixture?

A

GPa is converted into GPb and GSb is converted into GSa. This is because the presence of glucose switches GPa to the T state and causes it to release PP1/Gl complex and dephosphorylating the two enzymes.

Biochemistry 450 (3 decks)

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