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Biochemistry > Test 3 (chapter 22-31) > Flashcards

Test 3 (chapter 22-31) Flashcards

1
Q

What is the flow of electrons through the light reaction, starting with photosystem II? (7 steps)

A
  1. P680
  2. Electron transport chain (Ph, plastoquinones [Q])
  3. Cytochrome bf complex (QH2 –> Plastocyanin)
  4. P700* electrons replenished by Plastocyanin
  5. Electron transpot chain (chlorphyll, quinone, 4Fe-4S)
  6. Ferredoxin
  7. NADP+ [catalyzed by Ferredoxin-NADP+ Reductase]
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2
Q

What happens in Fixation stage of Calvin Cycle?

A
  1. [Rubisco] Ribulose 1,5-biphosphate + CO2 –> two 3-phosphoglycerate
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3
Q

What happens in reduction stage of Calvin Cycle?

A

Step 1: 2 3-Phosphoglycerate + 2 ATP -> 2 1,3-biphoshoglycerate + 2ADP

Step 2: 2 1,3-biphosphoglycerate + 2NADPH -> 1 Glyceraldehyde 3-phosphate 1 Dihydroxyacetone phosphate [These two are in equilibrium]

Step 3: Glyceraldehyde 3-phosphate or Dihydroxyacetone phosphate → Fructose 1,6-biphosphate

Step 4: 1 Fructose 1,6-biphosphate → Fructose 6-phosphate Glucose 6-phosphate Glucose 1-phosphate. [These three hexoses comprise the “Hexose monophosphate pool”]

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4
Q

What is the net reaction of regeneration stage of Calvin Cycle?

A

Fructose 6-phosphate +2 Glyceraldehyde 3-phosphate + dihydroxyacetone phosphate + 3ATP → 3 ribulose 1,5-biphosphate + 3ADP

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5
Q

What is the stoichiometry and energy cost of the dark reactions?

A

Three molecules of ATP and Two molecules of NADPH are used to bring CO2 to the level of a hexose. Six of these rounds are required for a total of 18 ATP, 12 NADPH and 12 CO2.

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6
Q

What are two ways the Calvin Cycle is regulated?

A
  1. Light reactions alter the environment of the stroma (decreased concentration of H+, NADPH, reduced ferredoxin) which increase catalytic activity of rubisco.
  2. Reduced ferredoxin activates thioredoxin by reduction, which in turn activates rubisco and other calvin cycle enzymes by reducing regulatory disulfide bonds.
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7
Q

What are the enzymatic steps of glycogen degradation?

A
  1. Phosphorylase
  2. Transferase
  3. Alpha-1,6-glucosidase
  4. Phosphoglucomutase (Convert G1P to G6P)
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8
Q

What enzymatic step of glycogen degradation only occurs in liver?

A

Glucose 6-phosphatase converts glucose 6-phosphate to free glucose, which can leave cell [enter blood].

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9
Q

What is the default state of glycogen phosphorylase in the liver?

A

Liver default is phosphorylase a in R state (most active)

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10
Q

What is the default state of glycogen phosphorylase in muscle?

A

Muscle default is phosphorylase b in T state (least active)

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11
Q

How is glycogen phosphorylase regulated allosterically in muscle?

A

Energy status:
• No exercise: ATP & Glucose 6-phosphate stabilize T state of phosphorylase b
•Exercise: AMP stabilize R state of phosphorylase b

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12
Q

How is glycogen phosphorylase regulated allosterically in liver?

A

Free glucose stabilizes T state (inactivation)… defaults to R state.

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13
Q

How is glycogen phosphorylase regulated by phosphorylation in muscle?

A

•Epinephrine causes phosphorylation and formation phosphorylase a which is always active.

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14
Q

How is glycogen phosphorylase regulated by phosphorylation in liver?

A

Hormonal regulation, based on presence of free glucose:
•Insulin promotes dephosphorylation (inactivation) [insult occurs when there is free glucose]
•Glucagon promotes phosphorylation (activation)

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15
Q

What are four (4) enzymatic steps of glycogen synthesis?

A
  1. UDP-glucose pyrophosphorylase converts glucose 1-phosphate to UDP-glucose
  2. Glycogen synthase transfers glucose of UDP-glucose to non-reducing end of glucose chain. But this can only happen if the chain is 4 glucose residues long.
  3. Glycogenin has two identical subunits with tyrosine residues that reciprocally attach 8 glucose molecules with alpha-1,4 bonds.
  4. Branching enzyme transfers 7 glucose residues to a glucose at least 4 away and converts alpha-1,4 bond to alpha-1,6.
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16
Q

What is the energy cost of making glycogen?

A

The cost of adding 1 glucose to a glycogen chain is 2 ATP.

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17
Q

What is the regulated enzyme of glycogen synthesis?

A

Glycogen synthase

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18
Q

What hormones regulate glycogen synthase and how?

A

1 .Glucagon/Epinephrine (promotes phosphorylation and deactivation)
2. Insulin (promotes dephosphorylation and activation)

19
Q

What other protein regulates glycogen synthase and how?

A

Protein Phosphatase 1; dephosphorylates, promoting activity.

20
Q

How is Protein Phosphatase 1 regulated?

A
  1. Epinephrine/Glucagon phosphorylation activity deactivates it.
  2. Insulin increases free glucose (inhibiting glycogen phosphorylase) and inactivates glycogen synthase kinase.
21
Q

What enzyme is mutated in McArdle disease?

A

Glycogen Phosphorylase

22
Q

What are the two stages of Pentose Phosphate Pathway and briefly describe them

A
  1. Oxidative phase: Glucose 6-phosphate oxidized to Ribulose 1,5-biphosphate and NAPDH
  2. Nonoxidative phase: Converts Ribulose 1,5-biphosphate to ribose, C-3, C-4, C-6 and C-7 sugars.
23
Q

What is the regulated enzyme in the oxidative phase of PPP?

A

Glucose 6-phosphate dehydrogenase

24
Q

What are the four key enzymes of the nonoxidative phase?

A
  1. Isomerase
  2. Epimerase
  3. Transaldolase
  4. Transketolase
25
Q

What is the primary mechanism of regulation of PPP?

A

High NADPH concentrations inhibit glucose 6-phosphate dehydrogenase.

26
Q

What are three (3) steps of triacylglycerol degradation?

A

Step 1: Epinephrine or Glucagon activate proteins that breakdown triacylglycerol into glycerol and fatty acid.

Step 2: Glycerol is transported to liver cells where it is put into glycolysis (forming pyruvate) or gluconeogenesis (glucose).

Step 3: Fatty acids are activated by CoA forming Acyl CoA, and will eventually be oxidized and incorporated into citric acid cycle.

27
Q

Describe Beta-oxidation

A

Four steps are repeated to oxidize the fatty acid CoA (Acyl CoA) to Acetyl CoA to be used in Citric Acid cycle. Each round of four steps produces Acetyl CoA and an Acyl CoA with a fatty acid chain shortened by two carbons.

28
Q

How are non-linear&saturated fatty acids degraded? (2 possibilities)

A
  1. Unsaturated fatty acids with an odd number of double bonds require isomerase.
  2. Even number of double bonds require isomerase and reductase.
29
Q

What are three (3) ketone bodies

A
  1. acetoacetate
  2. 3-hydroxybutyrate
  3. acetone.
30
Q

What are three (3) stages of fatty acid synthesis

A

Stage 1: Acetyl CoA transferred out of Mitochondria as Citrate. Citrate is cleaved into Acetyl CoA and oxaloacetate.

Stage 2: Acetyl CoA is activated to form Malonyl CoA [committed step]

Stage 3: Repeated addition and reduction of 2 carbon units onto molecular scaffold called acyl carrier protein.

31
Q

What is the enzyme for the committed step of fatty acid synthesis and what is its cofactor?

A

Acetyl CoA carboxylase & Biotin

32
Q

How is Acetyl CoA carboylase regulated? (4 ways)

A
  1. inhibited by AMP-dependent kinase (AMPK) [regulated by glucagon and epinephrine], and this is reversed by protein phosphatase 2A [regulated by insulin]
  2. activated by citrate and inhibits deactivation by phosphorylation
  3. inhibited by palmitoyl CoA [feedback inhibition]
  4. maloyl CoA inhibits carnitine acyl transferase, inhibiting fatty acid degradation
33
Q

What is the energy balance sheet for fatty acid degredation of a 18-C acid

A

Half as many acetyl CoA as carbons (9)
1 less NADH than acetyl CoA (8)
1 less FADH2 than acetyl CoA (8)

34
Q

What is a phosphatidate?

A

Two fatty acids added to glycerol 3-phosphate

35
Q

What is the regulated enzyme in the synthesis of phospholipids?

A

Phosphatidic acid phosphatase, which catalyzes the conversion of phosphatidate to diacylglycerol

36
Q

What are the head groups of sphingolipids used for?

A

Their head groups include sugars and sialic acid used in (1) cell recognition and (2) viral and bacterial attachment.

37
Q

What is the committed step of cholesterol synthesis?

A

[HMG-CoA reductase] acetyl-CoA –> mevalonate

38
Q

What are four (4) ways HMG-CoA reductase is regulated?

A
  1. Transcription control: sterol regulatory element binding protein (SREBP)
  2. Translation control: reductase mRNA controlled by metabolites of mevalonate
  3. Protein half-life control: Increases in cholesterol concentration result in the proteolytic degradation of the reductase.
  4. Control of enzymatic activity: Phosphorylation of the reductase by AMP-dependent kinase inactivates the enzyme.
39
Q

What are the role of transaminases and dehydrogenases in amino acid metabolism?

A
  1. Transaminases remove nitrogen from amino acids to another molecule (e.g. alpha-ketoglutarate, glutamate)
  2. Dehydrogenases remove nitrogen from a molecule like glutamate or glutamine.
40
Q

what are four (4) general processes of amino acid degradation

A
  1. 3 carbon (and tryptophan) AA transformed into pyruvate (citric acid cycle)
  2. 5 carbon AA converted into glutamate which is converted into alpha-ketoglutarate and used in citric acid cycle.
  3. Branched AA converted into acetoacetyl CoA and acetyl CoA and partially introduced into calvin cycle and converted into ketone bodies.
  4. Phenylalanine converted into Tyrosine with Phenylalanine hydroxylase. Tyrosine oxidized to acetoacetate and fumarate (citric acid cycle).
41
Q

What are two components of nitrogenase complex, the enzyme responsible for nitrogen fixation?

A
  • Reductase (dimer of iron-sulfur proteins) - transfers electrons from reduced Ferredoxin
  • Nitrogenase (hetero tetramer) - electrons flow from reductase to a molybdenum-iron-sulfur center which catalyzes nitrogen fixation (N2 -> NH3)
42
Q

What are the initial products made from ammonium from nitrogen fixation?

A
  • [Glutamate dehydrogenase] NH4(+) + Alpha-ketoglutarate → Glutamate
  • [Glutamine synthetase] Glutamate +ATP +NH3→ Glutamine
43
Q

What are the six (6) biosynthetic families of Amino Acids?

A
  1. [Citric acid cycle] → Oxaloacetate (ex. aspartate)
  2. [Citric acid cycle] → Alpha-ketoglutarate (ex. glutamine)
  3. [Glycolysis] → Pyruvate (ex. alanine)
  4. [Glycolysis] → 3-phosphoglycerate (ex. serine, glycine, cysteine)
  5. [Glycolysis and PPP] → Phosphoenolpyruvate and Erythrose 4-phosphate (ex. phenylalanine, tyrosine)
  6. [PPP] → Ribose 5-phosphate (ex. histidine)

Biochemistry (7 decks)

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