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BIOC 3300 > Week 3=> Electron Transport and OxiPhos, Mito Transporters, one-carbon and nuc meta > Flashcards

Week 3=> Electron Transport and OxiPhos, Mito Transporters, one-carbon and nuc meta Flashcards

1
Q

Where is most energy from ATP synthesis derived from?

A

From the oxidation of the reduced electron carriers made during glycolysis and the citric acid cycle

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2
Q

Hoe much NADH and FADH2 are generated per mole of glucose?

A

10 moles of NADH and 2 moles of FADH2

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3
Q

Where are the electron transport complexes bound?

A

Inner mitochondrial membrane

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4
Q

Why is the surface area of the inner mitochondria dramatically greater than the outer membrane?

A

Due to folds termed cristae

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5
Q

What does green fluorescent protein (GFP) label?

A

Mitochondria in cultured cells => specifically the mitochondrial cristae

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6
Q

What does magenta dye labelled?

A

Mitochondrial DNA

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7
Q

Mitophagy

A

Degradation of damaged mitochondria by the autophagy pathway

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8
Q

What is nutrient availability and mitochondrial efficiency coupled to?

A

Fission and fusion

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9
Q

Fission characteristic

A
  • Nutrient excess
  • Impaired OxPhos and ATP synthesis
  • Increased mito fission
  • Severe stress and mito damage
  • Between hyperfused and tubular morphology
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10
Q

Fusion characteristics

A
  • Nutrient limited
  • Increased OxPhos and ATP synthesis
  • Increased mito fusion
  • Mild stress
  • more fragmented (or short tubular) morphology
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11
Q

Mitochondrial complex that contains succinate dehydrogenase from the TCA cycle

A

Complex II

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12
Q

Mitochondrial complex that transfer protons into the intermembrane space

A

Complexes I, III, and IV

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13
Q

Mitochondrial complex that the ATP synthase couples proton import to ATP synthesis

A

Complex V

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14
Q

What shuttles bring NADH generated in the cytosol into the mitochondrial matrix?

A

DHAP/glycerol-3-phosphate shuttle or malate/aspartate shuttle

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15
Q

Enzymes, other proteins, and other cofactors involved in electron transfer complex I

A

Receives electrons from oxidation of NADH and passes to coenzyme Q (CoQ)

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16
Q

Enzymes, other proteins, and other cofactors involved in electron transfer complex II

A

Electrons from oxidations of succinate are passed to CoQ

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17
Q

Enzymes, other proteins, and other cofactors involved in electron transfer complex III

A

Oxidizes reduced to CoQ and reduces cytochrome C

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18
Q

Enzymes, other proteins, and other cofactors involved in electron transfer complex IV

A

oxidizes cytochrome c and reduces O2 to H2O

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19
Q

Faraday’s constant

A

96.5 kJ mol-1 V-1

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20
Q

ΔEo’

A

Difference in reduction potential between redox couples [Eo’(acceptor)-Eo’(donor)]

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21
Q

Exergonic

A

reactions release energy (-ΔG)(lower product)

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22
Q

Endergonic

A

reactions absorb energy (+ΔG)(higher product)

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23
Q

The standard free energy change (ΔGo) for the hydrolysis of for ATP under standard conditions?

A

31 kJ/mol

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24
Q

Describe the redox reactions in the respiratory chain?

A

Each redox reaction in the respiratory chain is exergonic and electrons from from low to high potential carriers

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25
Q

Coenzyme Q

A
  • hydrophobic electron carrier embedded in the inner mito membrane by long isoprenoid chain
  • Undergoes hydrogenation of ring carbons to alternate between and oxidized quinone (ketone) and reduced hydroquinone (alcohol)
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26
Q

Cytochromes

A
  • heme-containig proteins with distinct visible spectra based on the redox state
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27
Q

The efficiency of oxidative phosphorylation =

A

number of molecules of ATP synthesized per pair of electrons transported

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28
Q

Evidence of chemi-osmotic coupling

A
  • Proton and electrochemical (∆Ψ) gradients can be measured.
  • An intact inner mito membrane is required for coupling
  • Electron transport complexes span the membrane
  • Uncoupling agents dissipate the proton gradient
  • artificial generation of proton gradient permits ATP synthesis without electron transport
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29
Q

What dissipates the H+ Gradient?

A

Uncoupling agents

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30
Q

Which complex appears as a nod-like projection into the matric from the inner membrane of the cristae?

A

Complex V

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31
Q

What is the outer mitochondrial membrane (OMM) permeable to?

A

to molecules <10 kDa due to the voltage-dependent anion channel (VDAC)

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32
Q

How does VDAC work for the mitochondria?

A

VDAC closes when mitochondria are stressed and under hypoxic conditions

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33
Q

Hypoxic conditions

A

conditions where there is a lack of oxygen in the body or in the environment

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34
Q

What is the inner mitochondrial membrane (IMM) permeable to?

A

Is permeable to small, uncharged ad hydrophobic molecule s(water, oxygen, and CO2 pass easily)

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35
Q

What is the inner mitochondrial membrane (IMM) impermeable to?

A

Impermeable to large, charged, or hydrophobic molecules

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36
Q

Symport

A

solution is co-transport of ions of opposite charge

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37
Q

Antiport

A

Counter-transport of ions with same charge (preferred mechanism in most instances)

38
Q

ATP synthase/complex X

A

H+ into matrix

39
Q

Adenine nucleotide translocase

A

ATP towards OMM/cytosol, and ADP towards matrix

40
Q

Phosphate antiport

A

OH- towards OMM/cytosol, and H2PO4- towards matrix

41
Q

Phosphate symport

A

2H+ and HPO4 2- towards Matrix

42
Q

Pyruvate symport

A

2H+ and pyruvate towards matrix

43
Q

Dicarboxylate antiport

A

Dicarboxylate, HPO4 2- towards OMM/cytosol, and decarboxylate towards matrix

44
Q

Tricarboxylate antiport

A

Citrate towards OMM/cytosol, and Dicarbocylate towards matrix

45
Q

Solute carrier 25 (SLC25) family

A
  • Family of membrane proteins
  • Transport across IMM
  • 53 specificities
  • Most antiport
  • Encoded by nuclear genes and have common structure and mechanism
46
Q

What do SLC25 transport?

A

Phosphate, ADP/ATP, carboxylates, co-factors and amino acids acids the IMM

47
Q

Proton-coupled monocarboxylate transport system for pyruvate?

A

SLC16 family

48
Q

“Gate” steps for mechanisms of SLC25 solute antiport

A

1) Solute in cytosol
2) m opens and c closed => transition of solute from cytosol across IMM
3) solute released into matrix
2) c opens while m closes => solute from matrix transition across IMM
4) solute released into cytosol

49
Q

Most passively diffused by monocarboxylate transport across inner and outer membrane

A

acetate> propionate > beta-hydroxybutyrate > short-chain fatty acids

50
Q

SLC16

A
  • pyruvate carrier
  • major substrate for mitochondrial oxidation and is generated outside mitochondria
  • mechanisms of import is via a proton gradient driven symport (H+ and pyruvate anion cross membrane along the h+ ion gradient
51
Q

Monocarboxylate transporters

A

SLC25 and pyruvate carrier (SLC16)

52
Q

Dicarbocylate transporters

A

Malate carrier (SLC25S10) and alpha-ketoglutarate/malate transporter (SLC25A11)

53
Q

Tricarboxylate transport

A

Citrate carrier (SLC25A1 or CIC)

54
Q

SLC25A3

A
  • phosphate transport
  • At neutral pH there is a mic of HPO4 -2 and H2PO4- and passive diffusion will be slow or non-existent
  • Transport of H2PO4- in exchange for hydroxyl anion probably predominates in the intermembrane space
  • Presence of proton gradient favors the influx of phosphate in matrix via the symport or antiport mechanism
55
Q

Phosphate pKa

A

2.1, 7.2, 12.3

56
Q

Adenine Nucleotide Transporter (SLC24A4-6)

A
  • specific for ATP and ADP
  • most abundant mito membrane protein
  • Active as dimer of 30 kDa monomers
  • Strongly inhibited by low temp
  • transport regulated by the proton gradient, which in actively respiring mitochondria favors ADP uptake and ATP export from the matrix
57
Q

Specific inhibitors for Adenine Nucleotide Transporter (SLC24A4-6)

A
  • bonkrekic acid and carboxytractylate bind to matric (m) and cytosolic (C) exposed conformation of the permease, respectively
58
Q

SLC25A51

A

The IMM NAD+ transporter (because the IMM is impermeable to NADH and therefore “shuttle” mechanisms are used to transfer reducing equivalents across the inner membrane)

59
Q

Malate/Aspartate shuttle system

A

Active in liver and heart and coupled to the reduction of NAD to Mito

60
Q

Glycerol-3-phsophate/dihydroxyacetone phosphate (DHAP) shuttle

A
  • important shuttle in brain and muscle and coupled to FAD reduction
  • Glycerol-3-pohsphate is made by hydrolysis of triacylglycerol, which is prominent energy source of muscle. DHAP is a glycolytic intermediate
  • Enzyme is on external side of the IMM
  • Transfers electrons from FADH2 to Coenzyme Q of ETC
61
Q

Genetic defects in SLC25 transporters

A
  • 13 rare diseases related to mutations in SLC25 genes, all are autosomal recessive
  • Difficult to treat and often lethal. Organ transplants are performed in some cases
62
Q

Malate carrier (SLC25A10)

A
  • also has low affinity for oxaloacetate, fumarate and succinate
  • operates by an antiport mechanism; import of malate (or succinate) in exchange for HPO4 2-
  • Role is to supply malate that is the counter ion for the tricarboxylate transporter
63
Q

alpha-ketoglutarate/malate transporter (SLC25A11)

A
  • Important transporter for the import of reducing equivalents into mitochondrial matrix (coupled with glutamate/aspartate carrier)
  • Depends on reciprocal transport of phosphate
  • In isolation, a main function of the carrier is to generate glutamate in the cytoplasm
64
Q

Citrate Carrier (SLC 25A1 or CIC)

A
  • Antiport type carrier that exports citrate to the cytoplasm
  • Citrate export supplies cytosolic acetyl-CoA for fatty acid and cholesterol biosynthesis
  • Depends on conversion of citrate to malate in cytoplasm by ATP-citrate lyase; malate is then used for counter transport of more citrate
65
Q

One-carbon metabolism

A

Metabolic pathways that are connected to reaction involving the transfer of a single carbon (methyl group) in different oxidation states equivalent to methanol, formaldehyde, and formate

66
Q

Most important carriers of C-1 groups

A

Folic acid and S-adenosylmethionine

67
Q

What is S-adenosylmethionine a derivative of?

A

Methionine

68
Q

One-Carbon groups

A
  • Methanol (most reduced): methyl (-CH3)
  • Formaldehyde: methylene (-CH2-)
  • Formate (most oxidized): Formyl (-CHO) and methenyl (-CH=)
69
Q

What are two major medical conditions that Folate decreases prevalence of?

A

Spina bifida and Anecephaly

70
Q

Major carrier of 1-C units of amino acid and nucleotide metabolism?

A

Tetrahydrofolate (THF)

71
Q

How does THF work?

A

Carriers methyl groups in different oxidation states

72
Q

What is the source of the methyl group on THF?

A

Serine transfers a methyl-group to THF and is converted to glycine. Serine hydrocymethyltransferase

73
Q

SAM or AdoMet

A

s-adenisyl-homocysteine

74
Q

SAH or AdoHcy

A

S-adenosyl-homocysteine

75
Q

Major chemicals in the methionine cycle and methylation

A

1) Methionine
2) S-adenosyl-methionine
3) S-adenosyl-homocysteine
4) Homocysteine

76
Q

Methyltransferases reactions requiring SAM products

A
  • Phosphatidylcholine
  • Methylated proteins
  • Creatine
  • Other Methylated acceptors
77
Q

Requirements for one-carbon metabolism and methylation

A
  • folate
  • serine
  • Methionine
  • B6 Riboflavin
  • B12 Cobalamin
    Additional methyl groups from betaine (BHMT)
78
Q

What intermediate in 1-C pathways leads to production of both pyrimidines and purines?

A

5-methyltetrahydrofolate (5,10-CH3 THF)

79
Q

Important application of methylation reactions

A
  • DNA methylation
  • Phosphatidylcholine synthesis
  • Synthesis of carnitine, creatine, epinephrine, etc…
  • Purine synthesis
80
Q

DNA methylation application

A
  • Methylation of cytosine to 5-methylcytosine on CpG ‘islands”
  • Catalyzed by DNA methyltransferases (DNMT)
  • Inhibits transcription without changes in DNA sequence
81
Q

Nucleotide synthesis de novo pathway

A

Bases are synthesized from amino acids, CO2, folate derivatives and PRPP

82
Q

Nucleotide synthesis salvage pathway

A

Free bases from breakdown of nucleotide DNA or RNA react with PRPP

83
Q

PRPP

A

Phosphoribosyl-pyrophosphate (PRPP) = Activated Ribose 5-phosphate

84
Q

Pyrimidine nucleotide synthesis first forms ___

A

Uridine monophosphate (UMP)

85
Q

Purine nucleotide synthesis first forms ___

A

inosine monophosphate (IMP)

86
Q

Required substrates for IMP

A

PRPP, glutamine, glycine, aspartate, bicarbonate, methyl group for formyl tetrahydrofolate

87
Q

What are the two regulatory sites of Ribonucleotide Reductase?

A
  • One site to regulate overall activity
  • One site to regulate substrate specificity
  • This regulates of overall synthesis versus the relative amount of the different dNTPs
88
Q

Nucleotide Degradation

A

1) Phosphorylase acts on nucleoside to generate base and ribose-1-phosphate
2) Purines are degraded to uric acid, which is secreted in urine. Pyrimidines are degraded into amino acids

89
Q

What are purines degraded into?

A

Uric acid (for terrestrial reptiles, primates and many insects)

90
Q

What do “other” organisms do to further process uric acid before excretion?

A
  • Mammals (other than primates) ozidize uric acid to allantoin
  • Bony fish oxidize uric acid to allantoic acid
  • Cartilaginous fish and amphibian degrade allantoic acid to urea
  • Marine invertebrates decompose urea to NH4+

BIOC 3300 (11 decks)

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