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Biochemistry Pt. 2 > Everything Metabolism > Flashcards

Everything Metabolism Flashcards

1
Q

What is the first phase of glycolysis called?

A

The investment phase

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2
Q

What is NAD+ derived from? What biological reactions does it participate in? How many e- and H+ can it accept, respectively?

A

Vitamin B3 (niacin). Participates in bio oxidations (it gets reduced). Accepts 2 e- and 1 H+

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3
Q

What is pellagra?

A

Niacin deficiency - dermatitis, diarrhea, dementia, maybe death (Schaff called it D^3 or D^4)

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4
Q

What is the NAD+/NADH ratio in cells?

A

High

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5
Q

What enzyme of glycolysis exhibits negative cooperativity? What does that mean?

A

Glyceraldehyde-3-phosphate dehydrogenase. It means that it is NOT SENSITIVE to changes in substrate concentration

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6
Q

Under anaerobic conditions, how is NAD+ regenerated for glycolysis to continue?

A

Conversion of pyruvate to lactate.

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7
Q

What is hexokinase inhibited by?

A

Inhibited by G6P (its product) and 2-F-deoxyglucose

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8
Q

What intermediate do red blood cells take from glycolysis? What do they do with it?

A

They convert 1,3-BPG to 2,3-BPG (remember that 2,3,-BPG is an allosteric effector that reduces Hb affinity for O2)

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9
Q

What glycolytic enzyme(s) is/are arsenate toxic to?

A

G3P DH (PDH is also sensitive)

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10
Q

What toxin is enolase sensitive to?

A

Fluoride

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11
Q

Pyruvate kinase deficiency results in what? Why?

A

Anemia. Only one isozyme is present in red blood cells. If that one is mutated then that sucks.

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12
Q

What sugar-alcohol can result in retinopathy?

A

Sorbitol (causes increased ocular pressure - osmotic forces)

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13
Q

What two diseases can result from defective fructose metabolism? Which one(s) are serious?

A

Essential fructosuria is from fructokinase deficiency (benign b/c hexokinases can kinda do the job)
Hereditary fructose intolerance is from Aldolase B deficiency (SERIOUS b/c phosphates get used up in the phosphorylation of Fructose, then the pathway is stuck)

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14
Q

Which sugar is GALT enzyme involved in metabolizing? What disease results from GALT deficiency? Serious?

A

Galactose metabolism, disease is called CLASSIC GALACTOSEMIA. Phosphates get used up in the rxn galactose to gal-1-P, then pathway is stuck. Serious disease is in the newborn screen

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15
Q

What is UDP-gucuronic acid used for by cells and where does it come from?

A

Cells use it to make drugs and blilrubin more soluble for excretion. Comes from UDP-glucose.

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16
Q

What enzyme can combine UDP-glucuronic acid with drugs like benzoic acid to create more soluble substances? What disease results from deficiency of this enzyme?

A

UGT is the enzyme (UDP-alpha-D-glucuronyltransferase). Gilbert syndrome is the disease - eleveted bilirubin. Peeps usually asymptomatic.

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17
Q

Do obese people get drunk faster?

A

Yeah

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18
Q

What is the 2nd pathway that alcoholics have to metabolize ethanol?

A

MEOS Cyt P450 pathway.

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19
Q

What coenzyme is required for alcohol metabolism? What is the clinical significance of this? What disease results?

A

NAD+ is needed. Alcoholics often don’t eat, so they are deficient in niacin. Alcohol metabolism uses the little NAD+ available so glycolysis is halted as a result. Disease is called Wernickle-Korsakoff syndrome

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20
Q

A high NADH to NAD+ ratio results in the formation of what? (hint: think about what step NAD+ is required in glylcolysis and what side products can be made from the intermediate in the prior step). What population might have a problem with this?

A

DHAP/G3P can’t go to 1,3-BPG, so instead DHAP is converted into triglycerides. A problem amongst alcoholics

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21
Q

What is the cellular location of the TCA cycle?

A

Mitochondrial matrix

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22
Q

Thiamine/thiamin is also known as what (Vitamin _____)?

A

Vitamin B1

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23
Q

Describe pyruvate dehydrogenase, including its coenzymes, and the reaction it is involved in.

A

E1 (thiamine): Pyruvate comes in, gets decarboxylated (C02 leaves), acetate is the product.
E2 (lipoate): Takes acetate and combines it with CoA, which joins here. S-S bond is reduced. Acetyl CoA is the product and goes to TCA cycle.
E3 (FAD): Regenerates the enzyme (re-oxidizes the sulfur). FAD gets reduced to FADH2, and is oxidized back to FAD by NAD+ to NADH.

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24
Q

Small molecules can inhibit pyruvate dehydrogenase. How?

A

Small molecules like ATP, acetyl CoA, NADH, and fatty acids activate a kinase, which phosphorylates PDH, making it inactive.

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25
Q

What is Leigh’s disease? How is it treated?

A

Pyruvate dehydrogenase deficiency. Poor prognosis. Treatment is B1 supplement and kinase inhibitors (to try to keep PDH unphosphorylated and active)

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26
Q

What is special about aconitase?

A

It is stereospecific despite the fact that the reactant is symmetric.

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27
Q

Which TCA cycle enzyme uses the same coenzymes as pyruvate dehydrogenase? Therefore, what toxin is it sensitive to as well?

A

Alpha-KG DH - also sensitive to arsenic.

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28
Q

High insulin can lead to high citrate levels. What does citrate do when too much is made?

A

Citrate leaks out of the mitochondria into the cytoplasm where it inhibits PFK I and can also be made into fatty acids.

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29
Q

Define “anaplerotic pathway.”

A

Reactions that form intermediates of a metabolic pathway.

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30
Q

Name two heterozygotic TCA cycle enzyme defects.

A
  1. Succinate DH defect can cause phaeochromocytoma and paraganglioma.
  2. Fumarase mutations can cause predisposition to cutaneous and uterine leiomyomas and kidney cancers.
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31
Q

Where does the PP shunt occur in the cell?

A

Cytoplasm

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32
Q

What are two important products of the PP shunt and what is each one used for?

A
  1. Ribose-5-P for nucleotide synthesis.

2. NADPH is used to reduce glutathione for fatty acid synthesis and hydrogen peroxide reduction (superoxide metabolism)

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33
Q

Describe how NAD+ and NADP+ are different.

A

NADP+ has a phosphate group on it for enzyme-coenzyme recognition (different enzymes recognize it). It is B3 niacin-derived (NAD+ is B1 thiamin-derived). NADPH/NADP+ ratio is high so it can help with bio reductions(it gets oxidized - opposite of NAD+’s role)

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34
Q

How many carbons does a transketolase move? Transaldolase?

A

Transketolase - 2 carbons

Transaldolase - 3 carbons

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35
Q

What is the regulated, rate-limiting step of the pentose-phosphate shunt?

A

The first reaction (G6P to 6-phosphoglucano-delta-lactone by Glucose-6-P dehydrogenase)

36
Q

Describe the function of NADPH in protecting against oxidative damage.

A

The whole thing goes like this:

  1. Superoxides result from oxidation of hemoglobin
  2. Superoxide dismutase takes the superoxides and turns them into hydrogen peroxide.
  3. Hydrogen peroxide is converted to water, but this process requires the oxidation of glutathione. To get back reduced glutathione, NADPH is oxidized to NADP+. To get NADPH back, G6P is converted into G6P-delta-lactone in the PP shunt.
37
Q

How are superoxides used to our (humans) benefit? What enzyme is involved primarily? What disease is a result of the deficiency of this enzyme?

A

Used in the respiratory burst to kill bacteria. NADPH oxidase is used. Chronic granulomatous disease - frequent life-threatening infections.

38
Q

What results from Glucose-6-Phosphate Dehydrogenase deficiency?

A

Inability to regenerate NADPH, so oxidative damage goes unchecked. Heinz bodies form in RBCs from Hemoglobin disulfide bond formation - leads to dark urine and elevated bilirubin. RBCs are especially sensitive to this because THEY HAVE NO OTHER PATHWAY TO REGENERATE NADPH

39
Q

In what organs does gluconeogenesis occur?

A

80-90% in liver, 10-20% in kidney - more when starving

40
Q

In what subcellular locations does gluconeogenesis occur?

A

Mitochondria (pyruvate carboxylase reaction), cytoplasm, ER (G6Pase reaction).

41
Q

What enzymes can generate pyruvate from alanine?

A

Transaminases

42
Q

How to triacylglycerols enter the pathway for gluconeogenesis?

A

They are converted to DHAP, then through glycolysis to pyruvate, then oxaloacetate for gluconeogenesis.

43
Q

What are the three gluconeogenic enzymes that differ from the glycolytic enzymes?

A
  1. Pyruvate carboxylase
  2. PEP Carboxykinase
  3. Fructose-1,6-bisphosphatase
44
Q

What two amino acids is oxaloacetate converted to in the mitochondria so that gluconeogenesis can proceed in the cytoplasm? What are the byproducts of each conversion reaction?

A

Malate, aspartate. Malate generates NADH, aspartate converts alpha-KG to glutamate.

45
Q

What is Biotin?

A

The coenzyme that helps pyruvate carboxylase add C02 to pyruvate.

46
Q

Where is G6Pase located in the cell? Why?

A

In the ER lumen to prevent futile cycling

47
Q

What are the activators and inhibitors of Fructose-1,6-bisphosphatase?

A

Activated by citrate (leaked out from the mitochondria)
Inhibited by AMP and F-2,6-bisphosphate
(opposite of PFK I regulation!)

48
Q

What organs does glucagon target? What major organ does not have glucagon receptors?

A

Glucagon targets liver, adipose tissue. Muscles do not have glucagon receptors!

49
Q

What does the Cori cycle do?

A

Takes lactate from RBCs and Muscle, converts lactate back to glucose (using 6ATPs), and gives glucose back to RBCs and muscle.

50
Q

What is the Cahill cycle?

A

Pyruvate can be converted to alanine in muscle. Alanine goes to liver, gets converted back to pyruvate, then glucose (using 6 ATP), then goes in blood back to muscle.

51
Q

Name three reasons why glycogen is made.

A
  1. High glucose concentration would leak out of cells.
  2. High glucose concentration would cause osmotic problems.
  3. High glucose concentration would glycate everything.
52
Q

What two organs primarily participate in glycogenesis?

A

Liver, muscle.

53
Q

What does glycogen synthase need to work? How is this made?

A

It needs a polymer (primer), which is made from UDP-glucose and glycogenin to create a primer of ~7 glucoses attached to glycogenin.

54
Q

What are two benefits of glycogenin?

A
  1. Anomeric carbon participates in bonding so it can’t glycate stuff.
  2. Glycogenin-glucose chains get transferred to create 1,6 branches with branching enzyme.
55
Q

Describe the difference between glycogenolysis in muscle vs. in liver.

A

In both organs, glycogen -> G1P with glycogen phosphorylase, then G1P -> G6P with phosphoglucomutase.

  • In liver, glucagon is the driving hormone, which causes PFK2 phosphorylation (denying F-2,6-bisP formation, which would drive glycolysis). So instead, G6P goes to the ER and is made to glucose for release into the bloodstream, probably for the brain to take.
  • In muscle, there is no G6Pase, so it just uses G6P for energy metabolism for itself.
56
Q

What are the two forms of glycogen phosphorylase? Which is most active? How is it activated?

How does acetylcholine and Ca2+ affect this stuff?

A

Phosphorylase A vs. B.
A is phosphorylated and is more active. It is activated by glucagon:
1. Glucagon binds receptor.
2. G protein activation.
3. Adenylate cyclase converts ATP to CAMP, which activates Protein kinase A.
4. Protein kinase A phosphorylates a Phosphorylase kinase.
5. The phosphorylated kinase phosphorylates glycogen phosphorylase, making it active.

Acetylcholine activates Calcium which binds to the phosphorylase kinase to phosphorylate glycogen phosphorylase (making it type A - active), increasing glycogen breakdown.

-No joke.

57
Q

How does insulin affect enzymes involved in the glycogen pathway?

A

Insulin activates the phosphatase that removes the phosphate from glycogen phosphorylase A, turning it into phosphorylase B (less active - less glycogen breakdown). It also promotes the phosphatase that de-phosphorylates glycogen synthase, which activates the synthase, promoting glycogen synthesis!

58
Q

Glycogen synthase and glycogen phosphorylase are antagonistic enzymes that are activated/deactivated by phosphorylation. In which state (phosphorylated or not) is each active?

A

Glycogen synthase is ACTIVE when NOT phosphorylated.

Glycogen phosphorylase is ACTIVE when IT IS phosphorylated.

Remember that insulin PROMOTES PHOSPHATASES (removes phosphates). In the well-fed state, you want to make glycogen, so you would want both glycogen synthase and glycogen phosphorylase dephosphorylated.

59
Q

In general, what does epinephrine do to liver and muscle regarding glycogen?

A

Stimulates glycogen breakdown.

beta-adrenergic receptors in liver, alpha-adrenergic receptors in muscle

60
Q

How does Calcium levels in muscle affect glycogen metabolism?

A

It results in a 30-fold increase in phosphorylase kinase activity (phosphorylation of synthase inhibits glycogen synthesis, and promotes glycogen breakdown by glycogen phosphatase A)

61
Q

Is the outer mitochondrial membrane permeable? What about the inner membrane?

A

Outer is highly permeable (up to 10 kDa molecules). Inner is typically not permeable

62
Q

How many copies of mt DNA are present in each mitochondria?

A

2-10, and there are 10^3-10^4 mt/cell.

63
Q

Does mitochondrial DNA encode genes?

A

Yes, 37. 13 OXPHOS proteins, 2rRNAs, 22tRNAs.

64
Q

Is protein import critical for mitochondria? Why?

A

Yes! Nuclear DNA encodes 57 proteins that need to be imported into the mitochondria for use in OXPHOS.

65
Q

What mitochondrial complexes import proteins destined for the outer membrane, and inner membrane, respectively? Does the process use energy?

A

TOMs and TIMs. Evergy is used to unfold and re-fold the proteins so they can fit through the pores.

66
Q

A specific N-terminal sequence is found on proteins bound for which mitochondrial location?

A

Matrix-bound proteins (through the TIM)

67
Q

Roughly how many ATP are gained from OXPHOS?

A

~35

68
Q

What is the first step in OXPHOS? What are the 2nd and 3rd steps?

A
  1. Respiratory chain - transfer of electrons to 02
  2. Generation of proton transmembrane potential
  3. Proton motive force to generate ATP
69
Q

What two complexes in the respiratory chain participate in oxidations?

A

I (NADH oxidation) and II (FADH2 oxidation).

70
Q

Which respiratory chain complexes have proton pumps?

A

I, III, IV have pumps, II does NOT.

71
Q

How many ATP can be made from the energy gained from oxidation of NADH? How many protons are released? FADH2?

A

NADH releases 10 protons - good for 3 ATP

FADH2 releases 6 protons - good for 2 ATP

72
Q

What do the prosthetic groups do?

A

They carry out the redox reactions and are covalently or non-covalently associated with the respiratory chain proteins.

73
Q

What are the five prosthetic groups? (he said to rememer this!)

A
  1. Coenzyme NADH
  2. Flavin group (FAD, FMN)
  3. Coenzyme Q (ubiquinone)
  4. Heme (cytochromes b, c1, c, a, a3)
  5. Fe-S clusters
74
Q

Respiratory chain inhibitors exist for which complexes? Inhibition of which complexes will completely stop respiration?

A

Inhibitors exist for I, III, and IV. Inhibiting complex I does not result in complete respiratory inhibition because entry through complex II remains. Inhibiting III and IV does completely stop respiration.

75
Q

What does oligomycin do?

A

Inhibits ATP synthase aka complex V

76
Q

How does the ATP synthase work?

A

The kinetic energy from protons rushing through the complex results in a conformational change of the F1 ATP synthesizing centers, allowing ADP and Pi to form ATP.

77
Q

What do the electron shuttles do for OXPHOS? What are the two shuttles?

A

They bring electrons into the mitochondria for use in OXPHOS.

  1. Glycerol phosphate shuttle (irreversible) - no molecules cross the inner membrane
  2. Malate-aspartate shuttle - malate crosses the inner membrane. This one generates NADH (vs. FADH2 in the G phosphate shuttle) and is more favorable.
78
Q

What is coupling?

A

When respiratory chain reactions and ATP synthesis from complex V are linked.

79
Q

What is an example of physiological uncoupling?

A

Brown fat - heat production.

80
Q

What is mitochondria permeability transition?

A

A pathological condition in which the mitochondrial inner membrane becomes highly permeable.

81
Q

How is mitochondria permeability transition relevant to stroke and myocardial infarction? What molecule is thought to be responsible for it and how?

A

Inner membrane pores are acutely opened due to a calcium overload. Calcium binds to cyclophilin D, which is thought to open pores in the inner membrane. This creates an osmotic gradient, bringing in water and causing mitochondrial lysis.

82
Q

What is the deficiency in people with beri beri?

A

Thiamine (B1)

83
Q

What glycolytic intermediate can be converted to serine? What about alanine?

A

3-phosphoglycerate and serine can be interconverted. Pyruvate and alanine can be interconverted.

84
Q

Active transport of glucose takes place in intestinal epithelium and what other organ?

A

Kidney.

85
Q

Of the “other sugars,” which one is the only one that is phosphorylated at the 6 position in the first step of its metabolism?

A

Mannose

86
Q

Is the liver sensitive to insulin? What receptors do the liver have?

A

No, GLUT2 is not insulin-dependent.

Biochemistry Pt. 2 (9 decks)

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