Test 3 (chapter 22-31)

Question 1

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

Answer 1

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]

Question 2

What happens in Fixation stage of Calvin Cycle?

Answer 2

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

Question 3

What happens in reduction stage of Calvin Cycle?

Answer 3

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”]

Question 4

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

Answer 4

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

Question 5

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

Answer 5

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.

Question 6

What are two ways the Calvin Cycle is regulated?

Answer 6

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.

Question 7

What are the enzymatic steps of glycogen degradation?

Answer 7

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

Question 8

What enzymatic step of glycogen degradation only occurs in liver?

Answer 8

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

Question 9

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

Answer 9

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

Question 10

What is the default state of glycogen phosphorylase in muscle?

Answer 10

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

Question 11

How is glycogen phosphorylase regulated allosterically in muscle?

Answer 11

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

Question 12

How is glycogen phosphorylase regulated allosterically in liver?

Answer 12

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

Question 13

How is glycogen phosphorylase regulated by phosphorylation in muscle?

Answer 13

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

Question 14

How is glycogen phosphorylase regulated by phosphorylation in liver?

Answer 14

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

Question 15

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

Answer 15

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.

Question 16

What is the energy cost of making glycogen?

Answer 16

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

Question 17

What is the regulated enzyme of glycogen synthesis?

Answer 17

Glycogen synthase

Question 18

What hormones regulate glycogen synthase and how?

Answer 18

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

Question 19

What other protein regulates glycogen synthase and how?

Answer 19

Protein Phosphatase 1; dephosphorylates, promoting activity.

Question 20

How is Protein Phosphatase 1 regulated?

Answer 20

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

Question 21

What enzyme is mutated in McArdle disease?

Answer 21

Glycogen Phosphorylase

Question 22

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

Answer 22

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.

Question 23

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

Answer 23

Glucose 6-phosphate dehydrogenase

Question 24

What are the four key enzymes of the nonoxidative phase?

Answer 24

1. Isomerase
2. Epimerase
3. Transaldolase
4. Transketolase

Question 25

What is the primary mechanism of regulation of PPP?

Answer 25

High NADPH concentrations inhibit glucose 6-phosphate dehydrogenase.

Question 26

What are three (3) steps of triacylglycerol degradation?

Answer 26

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.

Question 27

Describe Beta-oxidation

Answer 27

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.

Question 28

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

Answer 28

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

Question 29

What are three (3) ketone bodies

Answer 29

1. acetoacetate 2. 3-hydroxybutyrate 3. acetone.

Question 30

What are three (3) stages of fatty acid synthesis

Answer 30

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.

Question 31

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

Answer 31

Acetyl CoA carboxylase & Biotin

Question 32

How is Acetyl CoA carboylase regulated? (4 ways)

Answer 32

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

Question 33

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

Answer 33

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

Question 34

What is a phosphatidate?

Answer 34

Two fatty acids added to glycerol 3-phosphate

Question 35

What is the regulated enzyme in the synthesis of phospholipids?

Answer 35

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

Question 36

What are the head groups of sphingolipids used for?

Answer 36

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

Question 37

What is the committed step of cholesterol synthesis?

Answer 37

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

Question 38

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

Answer 38

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.

Question 39

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

Answer 39

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.

Question 40

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

Answer 40

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).

Question 41

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

Answer 41

* 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)

Question 42

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

Answer 42

* [Glutamate dehydrogenase] NH4(+) + Alpha-ketoglutarate → Glutamate * [Glutamine synthetase] Glutamate +ATP +NH3→ Glutamine

Question 43

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

Answer 43

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)