Biochemistry- Enzymes/Reactions Flashcards

(86 cards)

1
Q

Glycosidase

A

Breaks glycosidic bonds

AKA Glycoside hydrolase

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2
Q

Iduronate sulfutase deficiency

A

Impaired degradation of GAGs (Dermatan sulfate and heparan sulfate affected)

  • Results in Hunter Syndrome (MPS II)
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3
Q

α- L iduronidase deficiency

A

Impaired degradation of GAGs (Dermatan sulfate and heparan sulfate affected)

  • Results in Hurler Syndrome (MPS I)
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4
Q

Sanfilippo syndrome mechanism

A
  • Missing enzyme for one of four steps to remove N-Sulfated/N-acetylated glucosamine residues from HEPARAN SULFATE
Depending on type, missing:
A- Heparan sulfamidase
B- N-acetyl glucosaminidase
C- Glucosamine- N- Accetyl transferase def.
D-  N-acetylglucosamino-6-sulfutase
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5
Q

ß- Glucuronidase definciency

A

Impaired degradation of GAGs (Dermatan sulfate and heparan sulfate affected)

  • Results in Hurler Syndrome (MPS VII)
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6
Q

Lactase deficiency

A
  • Intolerance of ingested milk products (Lactose intolerance)–> diarrhea, bloating, flatulence, increased H2 in breath

Can be congenital or due to intestinal injury

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7
Q

Sucrase-isomaltase deficiency

A

Ingested Sucrose intolerance

  • Impaired split of sucrose, maltose, maltotriose
  • -> diarrhea, bloating, increased H2 in breath
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8
Q

Fructose intolerance

A

Deficiency in GLUT-5

  • Can’t transport/absorb fructose (in large/moderate amounts)
  • GI distress, gas, H2 gas in breath

NOT the same as inability to metabolize fructose

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9
Q

I-cell disease

A

Deficiency in ability to phosphorylate mannose 6 (on a glycoprotein)

  • Glycoprotein can’t mark target enzymes to go to lysosome for destruction, so there is a bulidup of digestive enzymes in the cell
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10
Q

Reaction catalyzed by hexokinase?

- Cofactors/Requirements (if any)?

A

D-Glucose –> Glucose-6-phosphate

Irreversible, Step 1 of Glycolysis

  • NOT in liver/pancreas
  • Requirement: Mg 2+, ATP
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11
Q

Reaction catalyzed by glucokinase?

- Cofactors/Requirements (if any)?

A

D- Glucose –> Glucose-6-phosphate

Irreversible, Step 1 of glycolysis

  • In liver/pancreas ONLY
  • Requirement: Mg 2+, ATP
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12
Q

Reaction catalyzed by phosphofructokinase?

- Cofactors/Requirements (if any)?

A

Fructose-6- Phosphate –> Fructose-1,6-
bisphosphate

Irreversible, Rate limiting, and Committed step of Glycolysis (Step 3)

  • Requirement: Mg 2+, ATP
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13
Q

Reaction catalyzed by Glyceraldehyde 3- Phosphate dehydrogenase?
- Cofactors/requirements?

A

Glyceraldehyde-3-phosphate 1,3-bisphosphoglycerate

Reversible, not regulated (step 6 of glycolysis)

  • First NADH generated (x2)
  • Requirement: NAD+, Pi

Arsenate (arsenic poisoning) affects this step of glycolysis

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14
Q

Reaction catalyzed by Phosphoglycerate kinase?

- Cofactors/requirements?

A

1,3-bisphosphoglycerate 3-phosphogylcerate

Reversible, not regulated (step 7 of glycolysis)

** First substrate level phosphorylation, ATP generated (x2)

  • Requires ADP & Pi, Mg2+
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15
Q

Reaction catalyzed by pyruvate kinase (PK)?

- Cofactors/requirements?

A

Phosphoenolpyruvate –> Pyruvate

  • Irreversible, regulated (step 10 of glycolysis)

**Substrate level phosphorylation, ATP generated (x2)

-Requires: ADP, Pi, Mg2+, K+

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16
Q

How much ATP and NADH is generated during aerobic glycolysis?

A

2 ATP, 2 NADH

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17
Q

Reaction catalyzed by lactate dehydrogenase?

- Cofactors/requirements?

A

Pyruvate –> Lactate (reduction)

  • Last step in anerobic glycolysis

Requires: NADH

Lens/cornea, Kidney medulla, RBCs, testes, leukocytes all rely on anerobic glycolysis

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18
Q

Pasteur effect

A

The slowing of glycolysis in the presence of oxygen (b/c more ATP is produced)
- Glycolysis is faster under aerobic conditions

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19
Q

Reaction catalyzed by Enolase?

- Cofactors/requirements?

A

2-phosphglycerate PEP

Reversible & not regulated, Step 9 in glycolysis

  • Requirement: Mg2+
    Water is eliminated

Fluoride inhibits this enzyme, so bacteria in mouth produce less lactic acid, less cavities

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20
Q

Mechanism of Arsenic poisoning?

A
  • Affects glycolysis and TCA
  • In glycolysis, Arsenate gets incorporated into glyceraldehyde 3-phosphate –> forming 1-Arseno-3-phosphoglycerate
  • Hydrolyses spontaneously/easily to 3-phosphoglycerate b/c unstable
  • Bottomline: NO SUBSTRATE LEVEL PHOSPHORYLATION IN STEP 7, NO ATP GAIN, RBCS SUFFER BECAUSE CANT PRODUCE ATP
  • In the TCA–>
  • Arsenite inhibits enzymes requiring LIPOIC ACID (i.e. PDH, α-ketoglutarate dehydrogenase, branched-chain amino acid α–keto acid dehydrogenase)
    - Arsenite forms a stable complex with the thio group of lipoic acid
  • Affects the brain and cause neurologic disturbance and death
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21
Q

Regulation of glycolysis at step 1?

A

Inhibition:
- Negative feedback of glucose 6- phosphate (ONLY HEXOKINASE, b/c glucokinase has larger Km and less affinity, and larger V max)

Activation (indirect):
- Insulin stimulates GLUT 4 to come to cell membrane from inside cell, so intake of glucose into adipose (ie) cells increases

  • Hexokinase is active at low glucose levels compared to glucokinase
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22
Q

Regulation of glycolysis at step 10?

A

Allosterically activated:
- Fructose 1,6 bisphosphate (in liver, muscle 1&2, RBC by all 4 isozymes)- FEED FORWARD

Inhibition:

  • ATP (allosteric)
  • IN LIVER: glucagon decreases PK (pyruvate kinase) activity by phosphorylation
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23
Q

Regulation of glycolysis at step 3?

A

Activation (allosteric):
- AMP, ADP, Fructose-2,6-bisphosphate
F-2,6-BP is regulated by insulin/glucagon

Inhibition:
- ATP, citrate, high [H+]

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24
Q

Mechanism of Fructose-2,6-bisphosphate?

A
  • A VERY POTENT ACTIVATOR OF PFK-1 (step 3 glycolysis enzyme)
  • Also inhibits gluconeogenesis?

-Production is regulated by tandem enzyme: has Phosphofructokinase-2 (PFK-2) domain
AND Fructose-2,6-bisphosphatase (FBP-2) domain.

** In the presence of Insulin–> phosphotase active–> phosphotase dephosphorylates PFK-2–> PFK-2 (w/ATP) catalyzes phosphorylation from F-6-P to generate F-2,6-BP –> more activation of PFK-1 –>more glycolysis

** In the presence of glucagon –> Protein Kinase A is active –> PKA phosphorylates FBP-2–> FBP-2 removes phosphate from Fructose 2,6-BP (inactivates)–> less activation of PFK-1 –> less glycolysis

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25
Pyruvate kinase deficiency
- RBCs can't complete glycolysis (b/c need lactate to regenerate NAD+) - 50% less ATP produced - ATP is not available to regulate ION TRANSPORTERS - Hemolytic anemia occurs
26
Reaction catalyzed by Pyruvate dehydrogenase (PDH) complex? | Requirements?
Pyruvate --> Acetyl CoA Requires: - Thiamine pyrophospate (Vitamin B1) - E1 aka Pyruvate DEcarboxylase - Lipoic acid- E2 - CoA- E2 - FAD- E3 - NAD- E3 -CO2 is released (lost when TPP binds to pruvate, E1 domain)
27
What regulates PDH complex? What influences the regulators?
Inhibition: * PDH kinase (inhibits E1, less TCA)) - ATP, Acetyl CoA, and NADH activate the inhibitor (enough energy, less TCA) - Pyruvate INHIBITS the inhibitor (PDH kinase) -- not enough energy, more TCA Activation: * PDH phosphotase (activates E1) - Ca2+ released by skeletal muscle cells during contraction activates activator (need more energy, more TCA)
28
Reaction catalyzed by citrate synthase? | Requirements?
Oxaloacetate --> Citrate (Step 1 of TCA) Irreversible, regulated Requires: Acetyl CoA, H2O
29
Regulation of citrate synthase?
Inhibition: Citrate, NADH, Succinyl CoA
30
What does fluoroacetate inhibit?
Fluoroacetate is a rat poison/plant toxin - Inhibits Acitonase (Fe-S) enzyme that catalyzes Citrate to Isocitrate reaction (Step 2 of TCA)
31
Reaction catalyzed by isocitrate dehydrogenase? | Requirements?
Isocitrate --> alpha-ketoglutarate (step 3 of TCA) RATE LIMITING, irreversible, regulated Requires: NAD+ *1ST NADH YIELD, 1ST CO2 RELEASED
32
Reaction catalyzed by alpha-ketoglutarate dehydrogenase? | Requirements?
alpha-ketoglutarate succinyl CoA (step 4 of TCA) Requires: - Vitamin B1 (thiamine) - Lipoic Acid - CoA - FAD - NAD *2ND NADH YIELD, 2ND CO2 RELEASED
33
Regulation of Isocitrate dehydrogenase?
Activation: ADP, Ca2+ (in muscle) Inhibition: ATP, NADH Isocitrate --> alpha-ketoglutarate (step 3 of TCA)
34
Regulation of alpha-ketoglutarate dehydrogenase?
Activation: Ca2+ (muscle) Inhibition: ATP, NADH, GTP, Succinyl CoA alpha-ketoglutarate succinyl CoA (step 4 of TCA)
35
Reaction catalyzed by succinate thiokinase? | Requirements?
Succinyl CoA Succinate (step 5 of TCA, start of OAA regeneration) Reversible Requirements: GDP and Pi **GTP produced
36
Reaction catalyzed by succinate dehydrogenase? | Requirements?
Succinate Fumarate (step 6 of TCA) Reversible; Enzyme is in mitochondrial inner membrane (Complex II of ETC) Requirement: FAD **1ST AND ONLY FADH2 PRODUCED
37
Reaction catalyzed by Malate Dehydrogenase? | Requirements?
L-Malate Oxaloacetate (step 8 of TCA) Reversible; not very favorable but it's ok b/c step 1 of TCA is very favorable Requirement: NAD+ **3RD AND FINAL NADH GENERATED, REGENERATION OF OAA SO TCA WILL RESTART
38
How much ATP via equivalents is produced via TCA?
10-12 ATP (depending on tissue; brain and skeletal m. will produce less b/c they use glycerol phosphate shuffle)
39
PDH deficiency (E1 deficiency specifically)
Causes congenital lactic acidosis (because pyruvate gets reduced to lactate instead) - neurologic symptoms b/c brain is sensitive to lactic acidosis
40
Leigh syndromes (subacute necrotizing encephalomyelopathy)
- Either a PDH deficiency or a PC deficiency (30 possible gene mutations) Causes lactic acidemia and respiratory failure
41
Beriberi disease/Wernicke-Korsakoff syndrome (similar mech)
- Thiamine deficiency | cofactor of PDH, Alpha-ketoglutarate dehydrogenase
42
Reaction catalyzed by Pyruvate carboxylase (PC)? Requirements? Regulation?
Pyruvate --> oxaloacetate Irreversible - Oxidative step in gluconeogenesis to overcome step 10 in glycolysis - Also anapleroic reaction for TCA (restore OAA levels) Requirements: Biotin, ATP (x2), Mg2+, CO2 Takes place in mitochondria Regulation: allosterically activated by Acetyl CoA
43
Reaction catalyzed by phosphoenolpyruvate carboxykinase? | Requirements?
Oxaloacetate --> Phopsphoenol pyruvate Irreversible - Oxidative step in gluconeogenesis to overcome step 10 in glycolysis Requirements: GTP (x 2) - Note: CO2 is released 1/2 mitochondrial, 1/2 cytosolic in humans
44
Reaction catalyzed by fructose-1,6-bisphasphotase? | Requirements?
Fructose 1,6-bisphosphate --> Fructose 6-phosphate Irreversible - Oxidative step in gluconeogenesis to overcome step 3 in glycolysis Requirements: just H2O Phosphate released
45
Regulation of Fructose-1,6-bisphosphatase?
Inhibition: (allosteric) Fructose-2,6-bisphosphate (Insulin/Glucagon), AMP
46
Reaction catalyzed by glucose 6-phosphatase? | Requirements?
Glucose 6-phosphate --> Glucose Irreversible - Oxidative step in gluconeogenesis to overcome step 1 in glycolysis Requirement: just H2O Phosphate released **LIVER AND KIDNEYS ONLY RELEASE FREE GLUCOSE
47
What are reactions in gluconeogenesis that require ATP?
3-phosphoglycerate 1,3-phosphoglycerate (x 2) | Enzyme: Phosphoglycerate kinase
48
What are reactions in gluconeogenesis that require NADH?
1,3-phosphoglycerate glyceraldehyde 3-phospate (x2) | Enzyme: glyceraldehyde phosphate dehydrogenase
49
How much energy/reagents does gluconeogenesis require?
6 ATP, 2 NADH
50
What are the precursors of gluconeogenesis?
- Lactate (converted to pyruvate by Lactate DeHydrogenase) - alpha-keto acids and amino acids (from catabolism of glucogenic AAs, form oxaloacetate) - Glycerol (converted to glycerol-3-phosphate by glycerol kinase --> from hydrolysis of triglycerides)
51
What states result in gluconeogenesis regulation?
- Fasting - Prolonged exercise - High protein diet - Stress or injury - Substrate availability (lactate, pyruvate, glucogenic AAs, glycerol)
52
What is alcohol's effect on gluconeogenesis?
- Alcohol metabolism reduces NAD+ to NADH (NAD+ is needed for glycerol-P-dehyrogenase and LDH) - Less NAD+ means less gluconeogenesis and more lactate buildup - This can result in hypoglycemia and lactic acidosis
53
Which enzymes in the pentose phosphate pathway particpate in reactions that generate NADPH?
- Glucose 6-P dehydrogenase (G-6-P to 6-phosphogluco-delta-lactone)- 1st oxidative reaction ^(negative feedback from NADPH!!!) - 6-phoshogluconate dehydrogenase (6-phosphogluconate to ribulose 6-phosphate) - 3rd oxidative reaction
54
Glucose 6-P dehydrogenase deficiency mechanism
- Less NADPH--> less (reduced) glutathione--> more reactive oxygen species -> more damaged hemoglobin --> more hemoglobin aggregation --> Heinz bodies --> weak/fragile RBCs -->hemolysis (hemolytic anemia) NOTE: TOTAL absence is LETHAL, usually decreased activity
55
Reaction catalyzed by Glycogen phosphorylase? | Requirements?
Phosphorolysis of glycogen at alpha(1->4) linages using inorganic phosphate donation to oxygen of the glycosidic bond (glycogen breakdown) One residue at a time Irreversible, regulated Requirement: Vitamin B6 (PLP, pyridoxyl phosphate)
56
Reaction catalyzed by debranching enzyme?
Two functions (glycogen breakdown): - 4:4 glucan transferase: transfer 3 outer glucoses on branch to non-reducing end of chain - alpha-1,6- glucosidase removes remaining glucose that is alpha 1,6 linked (releases as FREE GLUCOSE, little)
57
Phosphoglucomutase reacton?
Converts glucose 1-P to glucose 6-P - At the end of glycogen phosphorylase's action, where only G-1-P remains - Also 1st step of glycogen synthesis - reversible reaction
58
Glucose-6-phosphate translocase action?
Enzyme that transports G-6-P into Endoplasmic Reticulum on LIVER/kidney cells - for release to body after broken down to free glucose Note: in muscle G-6-P is kept in cells for its own use
59
Reaction catalyzed by UDP-glucose phosphorylase? | Requirement?
Glucose 1-P --> UDP-glucose +PPi; 2nd reaction in glycogen synthesis UTP is required Also PPi breaks down to 2Pi
60
Reaction catalyzed by glycogen synthase? | Requirement?
UDP-glucose + Glycogen(n residues) --> Glycogen(n+1 residues) + UDP One unit at a time Requirement: Needs a "glycogen primer" of at least 4 residues
61
Reaction catalyzed by glycogenin?
Forms primer for glycogen synthesis - UDP-glucose + tyrosine on glycogenin --> glucose-o-tyrosine benzyl on glycogenin + UDP Makes 8mer primer, residues added on non-reducing end
62
Reaction catalyzed by (1,4-->1,6)- transferase?
- Branch formation on glycogen | - removes 6-8mer from non-reducing end, attaches it via 1,6 alpha linages, four residues from branch point
63
Glycolysis regulation actions for: - Glucose 6 phosphate - ATP - AMP - Glucose
- Glucose 6 phosphate: inhibits glycogen phosphorylase, activates glycogen synthase - ATP: inhibits glycogen phosphorylase - AMP: activate glycogen phosphorylase (MUSCLE ONLY; Ca2+ also activates glycogen breakdown via nerve stimulation only) - Glucose activate glycogen phosphorylase (LIVER ONLY)
64
Important enzymes in fructose metabolism
- Fructokinase: requires ATP, Fructose to Fructose 1-6-P - Aldolase B: Fructose 1-6-P to DHAP and Glyceraldehyde (Cause of hereditary fructose intolerance) Eventually gets converted to G3P, used in glycolysis
65
Important enzymes in sorbitol metabolism
- Aldose reductase: Needs NADPH; Glucose to Sorbitol (alcohol of fructose), produced when too much glucose - Sorbitol dehydrogenase: Need NAD+, Converts sorbitol to fructose - Often sorbitol accumulation is due to hyperglycemia
66
Important enzymes in galactose metabolism
- Galactokinase: ATP needed, Galactose to galactose-6-P - Galactokinase deficiency leads to increase galactose in blood and urine, galacticol accumulation, results in cataracts - Galactose 1-P Uridyl transferase: Needs UDP galactose (from UDP Glucose via epimerase); converts Galactose 1 P to Glucose 1 P - Deficiency results in classic galactosemia, can cause liver damage and other issues Then converted to glucose 6 P (phosphoglucomutase) for glycolysis/Glucose
67
Glycogen metabolism via Insulin (mechanism)
in liver and muscle * Stimulates cAMP phosphodiesterase - to decrease cAMP levels - reducing PKA activity * Increases hepatic protein phosphatase activity - this inhibits glycogen phosphorylase and its activator, phosphorylase kinase - stimulates glycogen synthase (via dephosphorylation) to increase glycogenesis
68
Glycogen metabolism via Glucagon (mechanism)
only in liver * stimulates G-protein - this stimulates adenylyl cyclase - increases cAMP - increases PKA activity - PKA phosphorylates and activates glycogen phosphorylase and phosphorylase kinase (its activator)
69
Glycogen metabolism via Epinephrine (mechanism)
* PKA path in muscle only, both PKA and PLC in liver * epi stimulates g-protein - G protein stimulates PKA - phosphorylation of glycogen phosphorylase and phosphoryl kinase (its activator) * epi also stimulates phospholipase C - PLC splits PIP2 to IP3 and DAG - DAG activates protein kinase C directly, inactivates glycogen synthase (via phosphorylation) - IP3 stimulates Ca2+ release to ER, which also activates PKC (which inactivates glycogen synthase) - Ca2+ also binds to calmodulin to activate calmodulin dependent kinase and phosphorylase kinase (which activates glycogen phosphorylase) - Calmodulin dependent kinase and phosphoryl kinase inactivate glycogen synthase
70
Lipase (FA breakdown)
- TAG to glycerol and fatty acids - Regulated by epinephrine and glucagon (because they activate PKA which activates hormone-sensitive lipase in the liver) - Insulin activates protein phosphatase 1 which inactivates HSL *Note: FA are carried in blood via albumin to rest of thebody
71
Thiokinase
- Converts FA to Fatty acyl CoA | - Requires ATP
72
Rate limiting step in fatty acid breakdown?
Carnitine shuffle in long chain fatty acid oxidation - In intermembrane space of mitochondria: Attaches Carnitine to FA CoA via CPT-1 (carnitine palitoyl transferase 1) to facilitate diffusion across inner mitochondiral membrane **CPT 1 is inhibited by Malonyl CoA (product during synthesis, Malonyl CoA in inhibited by high AMP and PKA) - Once in Mit membrane, CPT-2 converts back to fatty acyl coA
73
Fatty Acyl coA synthetase
- ATP + FA to FAcyl AMP + PPi to Fatty Acyl coA For intracellular activation of Fatty acyl coA
74
Acyl CoA Dehdrygeonases
Many Enzymes in reaction, convert Fattyl Acyl CoA to Enoyl CoA - B oxidation reaction, FA breakdown - Need FAD+, reaction produces FADH2
75
Enoyl CoA hydratase (general action)
Hydrolyses double bond in Enoyl CoA
76
3-hydroxyacetyl CoA dehydrogenase (general action)
Converts hydrated Enoyl coA (3-hydroxyacyl CoA) to ketone (3-ketoacyl coA) -Need NAD+, to produce NADH
77
Beta-ketoacyl-CoA (general action)
- Breaks up 3-ketoacyl CoA to a fatty acyl CoA (-2 Cs) and acetyl coA - The shorter FA COA is used for next round of beta oxidation (beta oxidation spiral) - Need CoA
78
What happens when breaking down odd # C FA chain?
- Last 3 cs released as Propionyl CoA - Converted to succinyl coA with three enzymes: 1. Propionyl CoA carboxylase (requires biotin, ATP, CO2) 2. Racemase- converts D to L isomer 3. Mutase- Converts to succinyl coA (needs vitamin B12)
79
HMG CoA Synthase
- EZ in ketone body synthesis - Converts Acetoacetyl Co A to 3-hydroxy-3-methyl glutaryl CoA ** RATE LIMITING STEP
80
HMG CoA Lyase
Converts 3-hydroxy-3-methyl glutaryl CoA (3HMG CoA) | to AcetoAcetate
81
D-Beta hydroxybutrate dehydrogenase
- AcAc to D-Beta hydroxybutrate (BHB) (NEED NADH) - AcAc also spontaneously releases acetone
82
Malic Enzyme
- Part of shuttle in FA synthesis to transport Acetyl CoA to cytosol from mitochondria (done by converting to citrate, then malate, then pyruvate) - small amount of NADPH produced in step (nothing much) - Converts Malate to pyruvate in cytosol (PDH will then convert it back to Acetyl CoA) Need NADP+
83
Acetyl CoA carboxylase
Converts Acetyl CoA to Malonyl CoA Malonyl CoA can inhibit CPT-1 in carnitine shuttle in FA breakdown ***RATE LIMITING STEP IN FA SYNTHESIS Needs Biotin - Activated by citrate, insulin - Inhibited by Palmitoyl CoA, AMP, Glucagon, Epinephrine
84
Fatty Acid Synthase
- 7 separate enzymes in complex that convert Malonyl CoA to Palmitate to Palmitoyl CoA! - Uses CoA for 2 additional Cs at beginning - EZ is a vitamin B derivative - Panothenic acid is also part of complex (transfers intermediates between sites on EZ complex) - Condensation, Decarboxylation, Reduction with NADPH x 2, dehydration reactions occur **ELONGATIon beyond 16 C occurs in smooth ER, similar mechanism as FA synthase, Malonyl CoA and NADPH needed
85
Where does desaturation of FA occur? What enzyme?
- In ER, can only form chains with CIS double bonds - Done by mixed function oxidase (desaturase) - Need NADH, O2, Cytochrome b5 For trans double bonds, we need linoleate and linolenate
86
Regulation of FA synthesis
A. Fed state: INSULIN↑, Fatty acid synthesis active, malonyl CoA blocks fatty acid transport into mitochondria, preventing FA oxidation B. Fasted state: GLUCAGON↑ , EPINEPHRINE↑ , INSULIN ↓; this activates Protein Kinase A via cAMP. 1. Hormone sensitive lipase is active via phosphorylation by protein kinase A 2. Acetyl CoA carboxylase is inactive (phosphorylated), preventing malonyl CoA formation. 3. Lack of malonyl CoA permits fatty acids transport (CPT-I) into mitochondria for oxidation.