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Biochem & Cell bio > Unit 19: TCA/Citric acid/ Krebs cycle; PDH rxn; Beta oxidation > Flashcards

Unit 19: TCA/Citric acid/ Krebs cycle; PDH rxn; Beta oxidation Flashcards

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Biology 101 flashcards
1
Q

describe mitochondria generally

A
  • where energy conversion happens
  • Hundreds to thousands per cell , depending
    on cell type
    – Many fused to one another
    – Some cells do not have mitochondria
  • has a Double membrane
    – Outer membrane controls entry of
    large molecules
    – Electron transport chain (ETC) and ATP synthesis enzymes located in inner membrane
  • need over 1000 different proteins for maintenance and function
  • most are encoded by nuclear genome and imported. some are encoded by mtDNA
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2
Q

describe mitochondria inner membrane

A
  • High content of cardiolipin and very protein-rich
  • Impermeable to ions and small charged molecules
  • Contains electron transport chain (ETC) and ATP Synthase
  • Contains protein importers (e.g., TIM), transporters and shuttles for small molecules and ions
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3
Q

describe mitochondria Outer membrane

A
  • Molecular sieve with channels formed by porins
  • Permeable for molecules < 5 kDa (in open state)
  • Enzymes for mitochondrial lipid synthesis located here
  • Import receptors and translocases for proteins (TOM complex) here
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4
Q

describe mitochondria Intermembrane space

A
  • Similar to cytoplasm in composition (small molecules)
  • Various enzymes exist here
  • the space between the outer membrane and inner membrane
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5
Q

describe mitochondria Matrix

A

Contains enzymes for several pathways
- pyruvate oxidation, TCA, amino acids, fatty acids, etc.

Contains mtDNA, transcription and translation components

  • inner most compartment
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6
Q

the TCA is the complete oxidation of fuel carbon backbone to CO2 with ____

A

electrons bound to carriers

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7
Q

Acetyl CoA (C2) is also know as

A

activated acetate

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8
Q

what is the first molecule to enter the TCA cycle

A

acetyl CoA

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9
Q

what are the catabolic and anabolic functions of TCA cycle

A

Catabolic:
- Provides electrons for oxidative phosphorylation
(3 NADH and 1 FADH2 per full cycle)
- Provides energy via substrate- level phosphorylation (1 step, 1 GTP)

anabolic:
- Provides precursors for building blocks

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10
Q

is the TCA cycle Amphibolic?

A

yes, has both catabolic and amphibolic pathways

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11
Q

what coupled cycles provide most of the energy from glucose oxidation

A

the TCA cycle and oxidative phosphorylation (ETC + ATP synthase)

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12
Q

do Fatty acids, glucose and Amino acids all feed into the TCA cycle?

A

yes, via acetyl coA

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13
Q

describe the PDH reaction

A
  • pyruvate transported into mitochondria matrix via mitochondrial pyruvate carrier (MPC)
  • Oxidative decarboxylation to acetyl CoA by PDH enzyme complex in the matrix
  • irreversible rxn
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14
Q

what is the net reaction of the PDH rxn

A

pyruvate + CoA + NAD = Acetyl CoA + CO2 + NADH + H+

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15
Q

what is the ∆𝐺′° of the PDH rxn

A

-8.0 kcal/mol

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16
Q

what is the PDH complex made of

A

E1: Pyruvate dehydrogenase (TPP)
E2: Dihydrolipoyl transacetylase (Lipoamide) + CoA
E3: Dihydrolipoyl dehydrogenase (FAD) + NAD+

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17
Q

what are the 5 coenzymes of the complex

A

TPP,
Lipoamide + CoA,
FAD + NAD+

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18
Q

what are the co-substrates of the PDH rxn?

A

CoA and NAD+

  • they are not tightly bound. they pick up molecules and leave
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19
Q

what are the prostethic groups of the PDH rxn

A

TPP (Pyruvate dehydrogenase) (E1)
Lipoamide (Dihydrolipoyl transacetylase) (E2)
FAD - dihydrolipoyl dehydrogenase (E3)

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20
Q

what are the apoenzymes of the PDH rxn

A

Pyruvate dehydrogenase
Dihydrolipoyl transacetylase
Dihydrolipoyl dehydrogenase

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21
Q

what does Pyruvate dehydrogenase do

A

takes away the CO2 and electrons

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22
Q

what does Dihydrolipoyl transacetylase do

A

something with the acetyl

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23
Q

what does Dihydrolipoyl dehydrogenase do

A

take the electrons away

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24
Q

describe general mechanism of PDH rxn

A

pyruvate decarboxylase
1. decarboxylation of Pyruvate
2. oxidation of acetyl group w/ simultaneous transfer to lkpoamide + formation of thioester bond

Dihydrolipoyl transacetylase
3. transfer of acetyl group from lipoamide to CoA + Preserves thioester bond

Dihydrolipoyl dehydrogenase
4. regeneration of lipoamide by oxidation of dihydrolipoamide
– Prosthetic FAD group as primary electron acceptor
– Electrons then transferred to NAD+

25
Q

what is the advantage of multi enzyme complex in performing consecutive reactions

A

Facilitates ‘substrate channeling’
Maximizes efficiency
Minimizes side reactions

26
Q

causes of PDH deficiency

A
  • Vitamin deficiencies (thiamine, niacin) due to nutritional deficits, alcohol abuse
    – Mutations of E1 component
    – Arsenic poisoning (inhibits lipoamide-containing enzymes)
27
Q

consequences of PDH deficiency

A
  • Lactic acidosis due to conversion of pyruvate to lactic acid
  • Severe CNS symptoms due to insufficient levels of ATP in CNS (relies on TCA cycle for energy production)
    • especially in mitochondria dense cells
28
Q

sources for fatty acids

A

triglycerides (adipose tissue)
dietary fats
acetyl CoA

29
Q

storage form of fatty acids

A

triglycerides-non polar storage in lipid droplets (adipocytes)

30
Q

enzyme that liberates FA

A

lipase- hydrolyzes the ester bond between oxygen and carboxyl group of hydrocarbon tail

31
Q

how are fatty acids activated

A

by binding to CoA

32
Q

triglycerides are __ for transport

A

solubilized
- bile salts for dietary lipids
- lipoprotein particles for blood transport of triglycerides
- albumin for FA

33
Q

how are FA activated

A

-bind to CoA
- enzyme is acetyl CoA synthase
- a mitochondrial outer membrane protein

34
Q

why is FA oxidation is called beta oxidation

A

b/c the beta carbon undergoes oxidation to a carbonyl group

35
Q

what is the fate of Glycerol from TG cleavage?

A

glycolysis - G3P

36
Q

FA oxidation in mitochondria vs. peroxisome

A

mitochondria:
- FA less than 20 carbons
- activation in cytoplasm and transported into mt
- b-oxidation to acetyl CoA
- complete oxidation to CO2 by TCA
- ATP regeneration by oxphos

peroxisome:
- for very long FA and branched
- activation in cytoplasm and transported into peroxisomes
- b-oxi to short FA and acetyl CoA
- direct reduction of O2 to H2O
- detox by Catalase
- export of NADH and Acetyl CoA; no ATP

37
Q

how are FA shuttled into one of the cellular compartments where oxidation takes place

A

via the carnitine shuttle
- it’s inhibited by malonyl-CoA
- a product of acetyl-Coa carboxylation at high levels of acetyl CoA

38
Q

net rxn of Mt FA Oxidation

A

Palmitate + 8 CoA + 1 ATP + 7 NAD + 7 FAD + 7 H2O = 8 acetyl Coa + 1 AMP + 2 Pi + 7 NADH + H + 7 FADH2

need 8 CoA, happens 7 times

39
Q

where does the acetyl CoA go and the NADH + FADH2 go

A

Acetyl CoA goes to TCA
NADH, FADH2 goes to OxPhos

40
Q

describe ketone bodies

A

produced by liver from acetyl CoA
– Alternate pathway for acetyl CoA metabolism
– Secreted into circulation

Fuel source for skeletal and
heart muscle, kidney
– Acetoacetate, hydroxybutyrate can be used by brain under starvation conditions

Produced in excess in diabetes, leading to acidosis (ketosis)

41
Q

function of the TCA cycle

A

produce NADH, FADH2

42
Q

is the TCA anaerobic or aerobic

A

TCA is aerobic but operates under anaerobic conditions
- O2 is required to progress for regenerating NAD/FAD via ETC

43
Q

What is the acceptor molecule for acetyl-CoA

A

oxaloacetate

44
Q

describe 1st rxn of TCA

A

-condensation rxn of acetyl CoA w/ oxaloacetate
-enzyme citrate synthase
-produces Citrate
- irreversible
- highly exergonic through hydrolysis energy-rich intermediate

45
Q

what pathway and enzymes are involved in replenishing oxaloacetate

A

gluconeogenesis
Pyruvate carboxylase and PEP carboxylkinase
-pyruvate carboxylase is activated by acetyl CoA

46
Q

replenishing rxns are called

A

anaplerotic

47
Q

irreversible steps of the TCA

A

step 1: enzyme citrate synthase

Step 4: isocitrate to a-ketoglutarate; enzyme isocitrate dehydrogenase

step 5: a-ketoglutarate to succinyl CoA; enzyme a-ketoglutarate dehydrogenase complex

48
Q

full cycle of TCA generates:

A

10 ATP/full cycle
– 1 GTP in TCA cycle via substrate level phosphorylation
– ~2.5 ATP/NADH+H+ via oxidative phosphorylation
– ~1.5 ATP/FADH2 via oxidative phosphorylation

49
Q

TCA net rxn

A

Acetyl CoA + 3 NAD + FAD + GDP + Pi + 2 H2O = 2 CO2 + CoA + 3 NADH + H + FADH2 + GTP

50
Q

controls of PDH

A

Inhibit:
- high levels of ATP, Acetyl CoA and NADH

Activate:
- high levels of AMP, CoA, Pyruvate

reversible modification (phosphorylation, dephosphorylation)
controls E1. phosphorylation inactivates

51
Q

controls of TCA

A

Isocitrate DH
– Inhibited by NADH
– Activated by NAD+
– Inhibited by ATP
– Stimulated by ADP
- Activated by Ca2+ (muscle)

α-Ketoglutarate DH
– Inhibited by HIGH succinyl CoA and NADH
– Activated by NAD+
– Inhibited by ATP
- Activated by Ca2+ (muscle)

Citrate Synthase
– Inhibited by citrate, succinyl CoA
(prokaryotic, mammalian in vitro)
Prokaryotes: – Inhibited by ATP and Stimulated by ADP

52
Q

pathway integration

A

Low energy charge
– Glycolysis, PDH and TCA becomes active
– Oxaloacetate reacts with Acetyl-CoA to citrate

High energy charge
– Glycolysis, PDH and TCA
becomes less active
– Conversion of oxaloacetate to glucose (gluconeogenesis)

53
Q

general steps for Beta oxidation of saturated FA and enzymes

A
  1. Dehydrogenation (oxidation
    - Acyl-CoA-Dehydrogenase
  2. Hydration
    - Enoyl CoA hydratase
  3. Dehydrogenation (oxidation)
    - L-3 hydroxyacyl CoA DH
  4. Cleavage (thiolysis)
    - β-ketothiolase
54
Q

which enzyme of the TCA is also a part of the ETC

A

Succinate dehydrogenase (complex II)

55
Q

which TCA intermediate is regenerated through anaplerotic rxn

A

Oxaloacetate

56
Q

what TCA rxns synthesize NADH, FADH2 and GTP?

A

Step: NADH

57
Q

what TCA rxn are substrate level phosphorylation

A

step 6: Succinyl CoA to Succinate; enzyme Succinyl CoA synthetase

58
Q

what TCA rxns are oxidative decarboxylation

A

step 4: isocitrate to a-ketoglutarate via isocitrate DH

step 5: a-ketoglutarate to succinyl CoA; enzyme a-ketoglutarate DH complex

59
Q

molecules synthesized for TCA intermediates

A
  • FA, Sterols
  • amino acids
  • porphyrins, heme

Biochem & Cell bio (20 decks)

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