Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

MCDB 310 > Chapter 16 (Cont.) -20 > Flashcards

Chapter 16 (Cont.) -20 Flashcards

1
Q

Step 1: Condensation

  1. What is the reaction?
    1. What is the enzyme?
    2. What goes into the reaction? What comes out?
  2. What is the activity of this reaction largely dependent on?
  3. Is it thermodynamically favorable/irreversible?
  4. What is it regulated by?
  5. How is citrate synthase unique?
A
  1. Acetyl-CoA + Oxaloacetate ⇒ Citrate
    1. Citrate Synthase, -32.2 kJ/mol, Rate determining step.
    2. H2O goes in, CoA-SH comes out.
  2. Largely dependent on Oxaloacetate
  3. Highly thermodynamically favorable.
  4. Regulated by substrate availability and product inhibition.
  5. It has an induced fit.
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

Step 2:

  1. What is the reaction?
    1. What is the enzyme?
    2. What goes in? What comes out?
  2. What does the elimination of water yield?
  3. Why must citrate be converted into isocitrate?
  4. Is the reaction thermodynamically favorable/irreversible?
  5. Water must be removed from citrate and then subsequently added to cis-aconitate. What is this catalyzed by?
  6. Only one version of isocitrate is produced by aconitase. What is this version?
A
  1. Citrate ⇔ Isocitrate
    1. Aconitase, 13.3 kJ/mol
    2. Water is released, then added to the formed intermediate.
  2. Gives a C-C double bond.
  3. Citrate, a tertiary alcohol, is a poor substrate for oxidation. Isocitrate, a secondary alcohol, is a good substrate for oxidation.
  4. Thermodynamically unfavorable/reversible. Product concentration kept low to pull forward.
  5. Only R-isocitrate is produced by aconitase. Distinguished by three-point attachment to the active site.
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

Step 3

  1. What is the reaction?
    1. What is the enzyme?
    2. What is made at this step? What is released?
  2. What is the alcohol oxidized to?
  3. What kind of enzymes use NADP+ as a cofactor?
  4. Is the reaction thermodynamically favorable/irreversible?
A
  1. Isocitrate ⇒ α-Ketoglutarate + CO2
    1. Isocitrate dehydrogenase, -20.9 kJ/mol
    2. NADPH is made, CO2 is released
  2. Alcohol is oxidized to a ketone. Transfers a hydride to NAD.
  3. Cytosolic isozymes.
  4. Highly thermodynamically favorable. Regulated by ATP and product inhibition.
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

Step 4

  1. What is the reaction?
    1. What is the enzyme?
    2. What is made at this step? What is released?
  2. After two turns of the cycle where do the carbons come from?
  3. What is unique about the product?
  4. Is the reaction thermodynamically favorable/irreversible?
  5. What is α-Ketoglutarate dehydrogenase?
A
  1. α-Ketoglutarate ⇒ Succinyl-CoA
    1. α-Ketoglutarate dehydrogenase
    2. NADH produced, CO2 released
  2. Carbons lost now come from oxaloacetate.
  3. Succinyl-CoA is a high energy thioester bond.
  4. Highly thermodynamically favorable/irreversible. Regulated by product inhibition.
  5. Complex similar to pyruvate dehydrogenase. Same coenzymes, identical mechanisms. Active sites different to accommodate different-sized substrates.
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

Step 5: Formation of GTP

  1. What is the reaction?
    1. What is the enzyme?
    2. What is made at this step? What is released?
  2. What kind of phosphorylation occurs at this step?
  3. What does the energy of the thiolester allow for?
  4. What is produced? What can it be converted to?
  5. Is the reaction thermodynamically favorable/irreversible?
A
  1. Succinyl-CoA ⇔ Succinate
    1. Succinyl-CoA synthetase, -2.9 kJ/mol
    2. GTP is made from GDP + Pi, CoA-SH is released
  2. Substrate level
  3. Allows for incorporation of inorganic phosphate.
  4. Produces GTP, which can be made into ATP.
  5. Slightly thermodynamically favorable/reversible. Product concentration kept low to pull reaction forward.
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

Step 6

  1. What is the reaction?
    1. What is the enzyme?
    2. What is made at this step? What is released?
  2. What is covalently bound to succinate dehydrogenase?
  3. What does FADH2 pass its electrons to?
  4. Where is this enzyme located? What is it part of?
  5. Is the reaction thermodynamically favorable/irreversible?
A
  1. Succinate ⇔ Fumarate
    1. Succinate dehydrogenase
    2. FADH2 is made at this step, 0 kJ/mol
  2. FAD is covalently bound
  3. To coenzyme Q
  4. In the inner mitochondrial membrane, part of Complex II of the electron transport chain.
  5. Near equilibrium/reversible. Product concentration kept low to pull forward.
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

Step 7

  1. What is the reaction?
    1. What is the enzyme?
    2. What is made at this step? What is released?
  2. How is this reaction sterospecific?
  3. Is the reaction thermodynamically favorable/irreversible?
A
  1. Fumarate ⇔ Carbanion transition state ⇔ L-Malate
    1. Fumarase
    2. -3.8 kJ/mol
  2. Addition of water is always trans and forms L-malate. OH- adds to fumarate… then H+ adds to the carbanion.
  3. Slightly thermodynamically favorable/reversible. Product concentration kept low to pull reaction forward.
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

Step 8

  1. What is the reaction?
    1. What is the enzyme?
    2. What is produced?
  2. What is regenerated at this step?
  3. Is the reaction thermodynamically favorable/irreversible?
A
  1. L-Malate ⇔ Oxaloacetate
    1. Malate dehydrogenase, 29.7 kJ/mol.
    2. NADH is produce.
  2. Oxaloacetate is regenerated for citrate synthase.
  3. Highly thermodynamically unfavorable/reversible. Oxaloacetate concentration kept VERY low by citrate synthase. Pulls the reaction forward.
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q
  1. What are anaplerotic reactions?
  2. Where is the citric acid cycle regulated?
  3. What are the general regulartory mechanisms?
A
  1. Intermediates in the citric acid cycle can be used in biosynthetic pathways (removed from cycle).
    1. Must replenish the intermediates in order for the cycle and central metabolic pathway to continue.
    2. 4-carbon intermediates are formed by carboxylation of 3-carbon precursors.
  2. Regulated at highly thermodynamically favorable and irreversible steps.
    1. PDH, citrate synthase, IDH, and KDH
  3. Regulatory Mechanisms
    1. Activated by substrate availability
    2. Inhibited by product accumulation
    3. Overall products of the pathway are NADH and ATP.
      1. Affect all regulated enzymes in the cycle
      2. Inhibitors: NADH and ATP
      3. Activators: NAD+ and AMP
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q
  1. How is pyruvate dehydrogenase regulated at E1?
  2. How do PDH kinase and PDH phosphorylase work?
A
  1. Regulation of E1:
    1. Phosphorylation: inactive
    2. Dephosphorylation: active
  2. Are part of mammalian PDH complex.
    1. Kinase is activated by ATP.
      1. High ATP → phosphorylated PDH → less acetyl-CoA.
      2. Low ATP → kinase is less active and phosphorylase removes phosphate from PDH → more acetyl-CoA
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q
  1. What is citrate synthesis also inhibited by?
    1. What is an important branch point for amino acid metabolism?
    2. What role does Succinyl-CoA play?
  2. What controls citrate levels?
    1. What does inhibition of IDH lead to?
A
  1. Citrate synthase is also inhibited by succinyl-CoA.
    1. α-ketoglutarate is an important branch point for amino acid metabolism.
    2. Succinyl-CoA communicates flow at this branch point to the start of the cycle.
  2. Regulation of isocitrate dehydrogenase controls citrate levels.
    1. Inhibition of IDH leads to accumulation of isocitrate and reverses acconitase. Accumulated citrate leaves mitochondria and inhibits phosphofructokinase in glycolysis.
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q
  1. How are plants versatile in biosynthesis?
  2. What kind of pathway is needed for carbohydrate biosynthesis in plants?
  3. Where do these reactions occur?
A
  1. Plants are extremely versatile in biosynthesis.
    1. Can build organic compounds from CO2.
    2. Can use energy of sunlight to support biosynthesis.
    3. Can adopt to a variety of environmental situations.
  2. Anabolic pathway: Uses ATP (energy) and NADPH (electrons) to convert CO2 into sugars.
    1. In plants: ATP is generated from light/photon absorption.
    2. NAPDH is generated by oxidation of H20 to O2 using light.
  3. Reactions occur in a specialized organelle, the chloroplast.
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q
  1. What kind of experiment did Calvin carry out?
  2. What was his first observation. What was the interpretation of this observation?
  3. What was his second observation. What was the interpretation of this observation?
A
  1. Incubated green algae with 14CO2 and traced the metabolic fate of 14C.
  2. First observation: within less than a minute, 14C-labeled amino acids and sugars were found → green algae are able to convert CO2 into small organic compounds (“CO2-assimilation”).
  3. Within 5 sec of incubation in 14CO2, labeled 3-phosphoglycerate (3-PG) was detected (C3-plants).
    1. 3PG is a stable intermediate.
    2. 3PG is formed by carboxylation of carbon intermediate.
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q
  1. What do autotrophic organisms use CO2 as a source of?
  2. How is CO2 reduced to carbon intermediates?
A
  1. Use CO2 as sole source for biosynthesis of starch, cellulose, lipids and proteins and other organic molecules.
  2. Use reducing equivalents of NADPH and energy (ATP), which is generated during photosynthesis to reduce CO2 to carbon intermediates.
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q
  1. What does three turns of the Calvin Cycle generate?

Step 1: CO2-Fixation

  1. What does this reaction consist of?
    1. What is the enzyme used?
    2. What does the active site of this enzyme contain?
    3. What is it coordinated by?
A
  1. 3 CO2, 9 ATP, 6 NADPH. All converted into 1 glyceraldehyde-3-phosphate.

Step 1: CO2-Fixation

  1. Carboxylation of ribulose 1,5 B-P to generate 2 molecules of 3-PG (catalyzed by ribulose 1,5 B-P carboxylase.
    1. Catalyzed by Rubisco - most abundant protein in the biosphere.
    2. Active site contains Mg2+​
    3. Mg2+ is coordinated by 3 AA side chain oxygens, including a carbamoylated Lys (-NH-COO-). Mg2+ forms coordinative bonds with both substrates, CO2 and Ru 1,5bP. Mg2+ orients and polarizes the substrates.
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

Step 2: Reduction

  1. What is the reaction?
  2. How does this step related to glycolysis?
  3. What cofactor is used?
  4. What can glyceraldehyde-3-P be used for?
  5. How is NADPH different from GAPDH?
  6. What is used to regenerate Ru 1,5 bP?
A
  1. 3-phosphoglycerate reduced to glyceraldehyde-3-P
  2. Reversal of glycolysis
  3. NADPH is being used instead of NADH, ATP is also used during this step.
  4. Uses of glyceraldehyde-3-P
    1. Stored as starch in chloroplast for later use.
    2. Translocated to cytosol and converted to sucrose (transported to non-photosynthesizing parts).
  5. Unlike GAPDH from cytoplasmic gluconeogenesis, stromal enzyme uses NADPH as co-factor.
  6. Majority of GA 3P is used to regenerate Ru 1,5 bP.
17
Q

Step 3: Regeneration

  1. What is the reaction?
  2. What step is this similar to in the PPP?
  3. What is the goal of this step?
  4. What are the pentose phosphates converted into?
  5. What phosphorylates Ru 5P → Ru 1,5 bP?
  6. What is the net reaction of the Calvin Cycle?
  7. What is the stochiometry problem?
A
  1. Regeneration of ribulose 1,5 bisphosphate starting from fruc-6-P.
  2. Very similar to the non-oxidative part of the pentose phosphate pathway except that it proceeds in the opposite direction = reductive pentose phosphate pathway (from hexose to pentose).
  3. Conversion of five three-carbon compounds (15 carbons) into three five-carbon compounds (15 carbons).
  4. Converted into Ru 5P
  5. Ru 5P kinase
  6. Picture
  7. The cycle will eventually run out of inorganic phosphate.
18
Q
  1. What does the Pi/Triose Antiport do?
  2. What else is this antiport used for?
A
  1. Export of triose phosphates for sucrose synthesis in the cytosol would soon deplete Pi pool in the chloroplast stroma → Pi -neutral antiport.
  2. Antiport is also used to transfer NAD(P)H and ATP produced by photosystems into the cytosol.
19
Q
  1. What does exposure to light produce?
  2. What happens when [H+] is pumped from the stroma into the thylakoid?
  3. What does high pH and Mg2+ in the stroma mean?
A
  1. Exposure to light → light reaction produces ATP and NADPH required for CO2 assimilation.
  2. [H+] is pumped from stroma into thylakoid → Mg2+ is exported in exchange.
  3. High pH and [Mg2+] in stroma
    1. Promote carbamoylation of Rubisco → activation.
    2. Activate chloroplast Frc 1,6bPase
20
Q

Calvin Cycle: Redox

  1. What does light exposure lead to?
  2. What does Fdred reduce?
  3. What happens in the dark?
A
  1. e- transfer from water → ferredoxin → NADP+
  2. Reduces thioredoxin (Trx), which in turn reduces S-S bonds in several enzymes of Calvin cycle → activation.
  3. O2 re-oxidizes SH groups and inactivates enzymes.
21
Q
  1. Why is there deleterious side-reactions of Rubisco?
  2. How often do these reactions occur?
  3. What how is this process challenging for plants in hot climates?
  4. How is the production of 2-Phosphoglycolate salvaged?
A
  1. Ru 1,5bP reacts with O2 instead of CO2.Consumes CO2 acceptor Ru 1,5 bP without achieving CO2 assimilation.
  2. One in every three or four turnovers – it forms 3-Phosphoglycerate and 2-Phosphoglycolate.
  3. Photorespiration increases with temperature.
  4. 2-Phosphoglycolate can undergo further reactions to to yield one triosephosphate and a CO2 but no energy is produced. Instead it consumes a lot of energy.
22
Q
  1. How do C3 plants differ from C4 plants?
  2. What is an additional problem in hot dry climates?
  3. What do CAM plants do?
  4. What happens at night?
A
  1. Plants discussed so far are called C3 plants: CO2-fixation results in formation of C3 compound (3-Phosphoglycerate). C4 plants: CO2-fixation and Rubisco activity are spatially separated (2 different cell types). Mesophyll cells: CO2 (HCO3-) is first used to synthesize oxaloacetate (C4 compound).
  2. Gas exchange via stomata (CO2 in, O2 out) results in loss of precious water.
  3. CO2-fixation (C4 cycle) and Rubisco activity occur in the same cell, but are temporally separated (2 different times).
  4. Stomata are open, CO2 (HCO3-) is used to form oxaloacetate → malate.

MCDB 310 (9 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions