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MBM > ATP Synthesis > Flashcards

ATP Synthesis Flashcards

1
Q

Structure of ATP? (slide 2)

A
  • Ribose with a nitrogenous base attached at 1’ C
  • three phosphate groups esterified at 5’ C
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2
Q

What energy bonds are more energy rich in ATP?

A

gamma and beta bonds (3rd and 2nd away from 5’)

-energy released from hydrolysis of gamma bonds is more, and used in many biological systems

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3
Q

What equation leads to the synthesis of ATP?

A

ADP + Pi = ATP

  • energy is neither created nor destroyed
  • energy must go in to create ATP
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4
Q

What process plays the most important role in ATP formation?

A
  • oxidative phosphorylation
  • substrate level phosphorylation plays a role but not as much ATP is formed
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5
Q

What organelle plays the most important role in ATP synthesis?

A

Mitochondria: powerhouse of the cell

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6
Q

Why does the number of mitochondria vary from cell to cell?

A
  • depends on energy need
  • 50% of cytoplasm of cardiac cells are filled with mitochondria, high energy
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7
Q

What cells do not have mitochondria? why?

A
  • RBCs
  • depends on substrate level phosphorylation through glycolysis for energy
  • only responsible to carry oxygen and CO2
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8
Q

Where does substrate level phosphorylation occur? oxidative?

A
  • substrate- in the cytosol
  • oxidative- in mitochondria (most of our energy)
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9
Q

Why is adipose tissue white? why is muscle red?

A
  • adipose tissue doesnt need energy, used for storage only, if you increase mitochondria the fat turns beige
  • muscle has a lot of mitochondria so it is red
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10
Q

Importance of outer membrane of mitochondria? inner membrane? inter membrane space?

A
  • outer- forms boundary of organelle
  • inner- is highly convoluted to form cristae (folds) to increase surface area and contains the mitochondrial matrix, many processes happen here
  • intermembrane space- contains cytoplasm to separate outer and inner membrane
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11
Q

What is the permeability difference between the outer and inner membranes?

A
  • outer- high permeability, so the contents of the inter membrane space is similar to the cytosol of the cell
  • inner- more impermeable to almost everything including H+, K+, Na+, ATP, ADP, and Pi (highly controlled)
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12
Q

What is the inner membrane and matrix rich in?

A

-rich in proteins/enzymes involved in different reactions including the electron transport system (ETS) and ATP synthase

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13
Q

What proteins form the ETS? systems? (slide 5)

A
  • four protein complexes called complex 1, 2, 3, 4 located in the inner mitochondrial membrane
  • 2 systems:

complex 1 -> complex 3(flavoprotein) -> complex 4(cytochrome)

complex 2 -> complex 3 -> complex 4

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14
Q

What is the electron donor for complex 1? complex 2?

A
  • NADH from the N side (matrix), from substrate
  • FADH2 from the P side (inter membrane space), or succinate (oxidized to fumarate)
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15
Q

How do complex 1 and 2 pass electrons to complex 3?

A
  • through coenzyme Q (free fluidity in membrane)
  • complex 1 has 8 Fe-S clusters, is large
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16
Q

After receiving electrons from complex 3, where does complex 4 donate its electrons?

A
  • to O2
  • H2O is formed from the reduced O2
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17
Q

When 2 H+ are taken from NADH by complex 1, how many H+ go into the inter membrane space?

A

4

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18
Q

Efficiency of complex 1 vs complex 2?

A
  • complex 1: 10 protons are pumped to the inter membrane space, (4 protons from complex 1)
  • complex 2: 6 protons are pumped to the inter membrane space, (no protons are pumped from complex 2)
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19
Q

What will chemicals that interrupt the electron transport system do? examples?

A
  • they will affect electron flow and ATP synthesis
  • cyanide and carbon monoxide are extremely toxic because they bind Fe in the heme complex 4, obstruct electron flow and block ATP synthesis
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20
Q

What is the significance of a configuration change in complex 1?

A
  • receives electrons from NADH, uses Fe and FMN
  • conformation changes which drives proton movement
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21
Q

Summary of the components of the ETS? (slide 9)

A

see chart

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22
Q

Another name for Coenzyme Q? properties? function?

A
  • ubiquinone
  • lipid soluble, can move in membrane -repeating sequences (6-10)
  • Q10 = energy supplement
  • collects electrons from complexes 1 and 2 and moves them to complex 3
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23
Q

What is a semiquinone? how does it form? (slide 10)

A
  • its a free radical, oxidative reactive species that can damage lipids, DNA, proteins
  • it forms because the reaction of CoQ happens one electron at a time
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24
Q

What is the driving force for ATP synthesis?

A

-electrochemcial potential

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25
Q

How is the electrochemical potential established? (slide 13)

A
  • protons are pumped by the ETS from the matrix to the inter membrane space
  • this pump provides an imbalance of H+ concentrations -positive outside inner membrane, more acidic
  • negative inside matrix
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26
Q

Why is it called electrochemical potential?

A
  • electro- because of membrane potential (positive vs negative)
  • chemical- because it involves protons
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27
Q

Where is ATP synthase (complex 5) located? domains? (slide 14)

A
  • big protein complex located in the inner mitochondrial membrane
  • domains: Fo and F1
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28
Q

What is the Fo domain of ATP synthase?

A
  • composed of 12 peptide subunits (C subunits), each has a proton binding site
  • forms a pore or channel in the membrane through which H+ returns to the matrix (H+ channel), it is embedded
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29
Q

What is the F1 domain of ATP synthase?

A

-catalytic domain (a, b, alpha, beta, gamma, delta)

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30
Q

What is the process (steps) of ATP synthase that leads to ATP synthesis?

A
  1. proton current drives the Fo domain (C complex) and the gamma subunit of F1 (actin filament binds)
  2. conformational change of F1, rotate around, different conformation of game subunit tells alpha and beta subunit (3 alpha/beta) to the do the next three steps
  3. bind substrate Pi and ADP
  4. synthesize ATP
  5. release ATP product (3 ATP)
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31
Q

How many ATP are synthesized from the rotation of ATP synthase? How many protons are required to rotate the Fo complex? (slide 15)

A
  • 3 ATP
  • 12 protons are needed to rotate Fo for a full circle
  • so to synthesize one ATP, you need 4 protons
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32
Q

What is the oxidation step in oxidative phosphorylation? (slide 21)

A
  • the coenzymes or reducing equivalents (NADH, FADH2) get oxidized, electrons transferred through ETS and are accepted by O2
  • protons are pumped simultaneously to the inter membrane space from the matrix and electrochemical potential is established
  • complex 1 to 3 to 4
33
Q

What is the phosphorylation step in oxidative phosphorylation?

A

-ADP is phosphorylated to ATP by ATP synthase using the electrochemical potential as driving force

34
Q

How many ATP molecules are synthesized when a NADH oxidizes through complex 1 to form a water molecule?

A

2.5 NADH leads to 10 H+ being released, you need 12 to make 3 ATP, so 4 H+ per ATP 10/4= 2.5

35
Q

How many ATP molecules are synthesized when a succinate is oxidized through complex 2 to form water?

A

1.5 Succinate leads to 6 H+ 6/4= 1.5

36
Q

Adenosine nucleotide translocase function? (slide 24)

A
  • antiporter- ATP and ADP go in opposite directions
  • transports one ATP from matrix to cytosol
  • transports one ADP from cytosol to matrix
37
Q

Why do we need transporters in the mitochondria?

A
  • ATP is synthesized in the matrix, but is needed outside of the mitochondria, but the inner membrane is impermeable to ATP, so something needs to transport it out
  • similarly ADP is outside the inner membrane and needs to get into the matrix to synthesize ATP
38
Q

Transporter function of ATP synthase?

A
  • mediates protons flowing into matrix to generate ATP
  • uniporter
39
Q

Phosphate translocase function?

A
  • bring phosphate back to the matrix from inter membrane space
  • symporter- H+ and Pi move in same direction
40
Q

Interconversion of energy in ATP synthesis?

A
  1. oxidation/reduction (chemical energy)
  2. electro chemical gradient (potential energy)
  3. phosphorylation of ADP to ATP (kinetic energy)
41
Q

Reducing equivalent definition?

A
  • 1 hydrogen atom
  • 1 proton, 1 electron = H or H+ + e
  • carried by different molecules (NAD, NADP, FAD, FMN)
42
Q

Where are NAD+ (nicotinamide adenine dinucleotide) and NADP+ (nicotinamide adenine dinucleotide phosphate) derived from? (slide 27)

A
  • derived from Vitamin B3 (niacin)
  • can also be synthesized from tryptophan (needs Vit B6)
  • nicotinamide is active site (oxidized), positive charge in ring in this form
43
Q

Vitamin B3 (niacin) deficiencies?

A
  1. Glossitis- inflammation of tongue, swelling or color change
  2. severe deficiency leads to Pellagra:
    - diarrhea
    - dermatitis
    - dementia
    - Hartnup disease- poor absorption of non polar AAs, reduced tryptophan ability
    - Malignant carcinoid syndrome- increased tryptophan metabolism (formation of serotonin)
    - INH users for the treatment of TB- Vit B6 deficiency, side effect
44
Q

Excess Vit B3?

A

facial flushing due to pharmacological doses for treatment of hyperlipidemia

45
Q

What are Vit B2 derivatives? (slide 30)

A
  • FMN (flavin mononucleotide)
  • FAD+ (flavin adenine dinucleotide)
  • transfer two H+ to make FADH2 or FMNH2
46
Q

Vit B2 deficiency?

A
  • cheilosis- inflammation of lips, scaling, and fissures at the corners of the mouth
  • corneal vascularization
47
Q

What three biological fuels are the reducing agents mainly generated from?

A
  1. Carbohydrates (glucose, other sugars)
  2. Fats (fatty acids and glycerol backbone)
  3. Proteins (amino acids)
    - ethanol is also energy rich and contributes reducing equivalents
48
Q

During starvation, what serves as the major substrate for muscle and brain?

A

ketone bodies

49
Q

Summary of the process of oxidation of food, generation of reducing equivalents, ATP synthesis? (slide 33)

A
  1. conversion to Acetyl CoA
  2. Oxidation of Acetyl CoA via TCA cycle
  3. generation of reducing equivalents
  4. synthesis of ATP
50
Q

What is the common terminal product of different catabolic paths? (slide 34)

A
  • Acetyl CoA -different fuels have different efficiencies in generating it
  • fatty acids- metabolism through beta oxidation, cut off two C’s each time to generate it, very efficient
  • glucose- not as much energy as fat, low energy
  • ketone bodies- 4 C to generate 2 Acetyl CoA, high energy
  • amino acid- not as efficient, low energy
  • alcohol- high energy molecule
51
Q

Coupling of energy expenditure to energy production? (slide 35)

A. energy requiring processes

B. ATP synthesis

A

A. Energy requiring processes:

  • anabolism (synthesis)
  • mechanical work (muscle contraction)
  • active transport

B. ATP synthesis:

  • substrate level phosphorylation
  • oxidative phosphorylation
  • ATP synthesis and usage are two processes coupled together
52
Q

What is the solution to the problem of NADH not being able to cross the inner mitochondrial membrane?

A
  1. Malate Aspartate shuttle (liver)
  2. Glycerol-3 phosphate shuttle (brain)
    - carry the reducing equivalent (H+ + e) but not the NADH molecule across the membrane
    - choice of shuttle depends on appropriate enzymes
53
Q

What are the two enzymes used for the Malate Aspartate shuttle?

A
  1. Malate Dehydrogenase
  2. Aspartate Aminotransferase
54
Q

What are the two transporters used for the Malate Aspartate shuttle?

A
  1. Malate-alpha ketoglutarate
  2. Glutamate aspartate transporter
55
Q

Process of Malate Aspartate shuttle? (slide 36)

A
  1. NADH reduces oxaloacetate (OAA) to malate by malate dehydrogenase in cytosol
  2. Malate enters the mitochondria through the malate/alpha-ketoglutarate transporter (anti porter)
  3. in the matrix, malate is re-oxidized back to OAA by mitochondrial dehydrogenase (malate dehydrogenase)
  4. NADH by this reaction is the mitochondria enters the ETS and 2.5 ATP are generate per NADH
  5. OAA cannot cross the membrane so it is transaminated to aspartate by the Aspartate Aminotransferase (Glutamate Oxaloacetate Transaminase in mitochondria)
  6. Aspartate is sent back to the cytosol by the Asparate-Glutamate transporter
  7. in cytosol, aspartate is deaminated to regenerated OAA for the cycle to continue
    - this system shares some substrates with the TCA cycle
56
Q

Process of Glycerol-3-Phosphate shuttle? (slide 37)

A
  1. Dihydroxy acetone phosphate (DHAP-produced in cytosol during glycolysis) is reduced to glycerol-3-phosphate (G3P) by NADH
  2. G3P can now cross the outer membrane of mitochondria
  3. G3P is oxidized to DHAP in the inner mitochondrial membrane by the enzyme G3P dehydrogenase (outer side of inner membrane) that transfers electrons to FAD to form FADH2
  4. FADH2 passes its 2 electrons to Complex 3 in the electron transport chain, which generates approximately 1.5 ATP for each FADH2 (6 protons generated)
  5. DHAP is regenerated and returns to the cytosol for the cycle to continue
    - different number of ATP molecules will be generated from a cytosolic NADH depending on which shuttle is used
    - no matter which shuttle is used, only the reducing equivalents (electrons and protons), not the NADH itself, are transferred across the mitochondria membrane
57
Q

What is the role of ADP in respiratory control? how? (slide 39)

A
  • stimulates respiration
  • addition of ADP speeds up oxygen concentration reduction dramatically
  • when all ADP has been converted to ATP (ADP=0), oxidative phosphorylation slows down significantly
58
Q

What ratios control oxidative phosphorylation? how? (slide 39)

A
  • ADP/ATP and NAD/NADH ratios
    1. ADP is phosphorylated to ATP, ratio of ADP/ATP becomes lower
    2. phosphorylation pulls protons through ATP synthase into the matrix
    3. use of protons from the cytosolic side for ATP synthesis decreases the proton gradient
    4. the ETS pumps more protons and O2 is reduced to water, decreasing the O2 concentration
    5. as NADH donates electrons to the ETC, NAD+ is generated and the NAD/NADH ratio is high, NAD+ serves to stimulate the TCA cycle
  • ADP/ATP and NAD/NADH regulate ETC, and oxidative phosphorylation, and TCA cycle
59
Q

What does oligomycin do? how?

A
  • inhibits ATP synthase
  • it binds to the Fo of ATP synthase and prevents the movement of H+ through the proton channel, so no ATP is synthesized
  • enhances ETS with elevated electrochemical potential
  • H+ gradient builds up and the ETS slows down and stops
  • it does not inhibit respiration directly, but prevents dual stimulate by ADP
  • higher ADP/ATP, lower ATP levels
  • an uncoupler can still stimulate oxygen consumption in the presence of oligomycin
60
Q

During oxidative phosphorylation, what two things happen simultaneously? uncoupler? (slide 41)

A
  1. ETC reaction which also pumps H+ form the matrix to the inter membrane space build up the electrochemical potential
  2. ATP synthesis catalyzed by ATP synthase using potential driving force
    - anything that can disconnect these two processes is an uncoupler
61
Q

What is DNP? (slide 42)

A
  • Dinitrophenol
  • synthesized uncoupler
  • weakly acidic and hydrophobic
  • has a phenolic hydroxyl group which can be either protonated in the intermembrane space or deprotonated in the matrix depends on the environmental pH
  • increases H+ in the matrix, disrupts H+ gradient
62
Q

How does DNP act as an uncoupler? (slide 42)

A
  1. in the inter membrane space where H+ is high, DNP is protonated
  2. protonated DNP, being lipophilic, diffuses to the mitochondrial matrix
  3. in the matrix, where H+ is lower, DNP is deprotonated, depositing protons there
  4. the deprotonated DNP is now favored to move back to the inter membrane space b/c of its lipophilic property and the electrochemical potential (positive inter membrane space)
  5. this process counteracts the H+ pump and disrupts the electrochemical potential quickly
  6. ETC chain proceeds, but ATP is not synthesized
63
Q

What are two uncouplers of oxidative phosphorylation and the ETC? (slide 43)

A
  1. DNP- destroys H+ gradient, allowing continued ADP stimulation of O2 consumption to try to restore proton gradient w/o ATP synthesis
  2. oligomycin- inhibits ATP synthase, intact proton gradient increases, slows rate of ETS, slows O2 consumption
64
Q

What is thermogenin? what does it do? (slide 44)

A
  • located on inner membrane of mitochondria -uncoupling protein of H gradient, UCP
  • oxidation of NADH and FADH2 -can mediate proton to get into matrix, forms H-gradient
  • reduces ATP synthesis and generates heat (different levels)
  • hibernating animals and brown adipocytes of newborns have higher concentration
  • regulated by thyroid hormone, norepinephrine
  • hyperthyroidism- higher concentration enhances expression of thermogenin, more heat
65
Q

Summary of regulation of ATP synthesis?

A
  • ADP is required for ATP synthesis
  • ATP hydrolysis controls ATP synthesis
  • ADP effects:
  • enhances oxidative phosphorylation
  • increases rate of TCA cycle allosterically
  • NADH is required for ATP synthesis
  • NAD+ is required for TCA cycle
  • energy needs (which consume NADH) allow NAD to increase rate of TCA cycle
  • as energy declines, excess NADH slows TCA cycle
  • ratios ATP/ADP and NADH/NAD+ determines rate
66
Q

Interlocking regulation? (slide 46)

A
  • Glycolysis
  • Pyruvate oxidation
  • Citric acid cycle
  • oxidative phosphorylation all regulated by relative concentrations of:
  • ATP -ADP -AMP -NAD+ -NADH
67
Q

What determines ADP/ATP ratio?

A

ATP usage

68
Q

Elevated ADP/ATP ratio?

A
  • increased ETS
  • increased TCA
  • increased catabolism
  • increased macronutrient degradation
69
Q

Reduced ADP/ATP ratio?

A
  • decreased ETS
  • decreased TCA
  • increased anabolism
  • increased macromolecule synthesis
70
Q

What did the calorie restriction (CR), NAD/NADH and longevity study show?

A
  • CR increases longevity
  • during CR, Sirt1 (deacetylase of histones) activity increases, changes expression of DNA, longer lasting effect
  • NAD serves as an Sirt1 activator
  • increased NAD/NADH enhances Sirt1
  • lowers cholesterol, fasting glucose, and blood pressure
  • slows down aging, increases longevity
71
Q

What is Resveratrol?

A
  • natural product
  • enriched in peanuts, mulberries, grapes, red wines
  • similar effects to calories restriction
72
Q

ATP Synthase uses electro-chemical potential to

A. Pump H+ from mitochondrial matrix to the inter- membrane space

B. Pump H+ from cytosol to the inter-membrane space

C. Synthesize ATP and mediate H+ influx to the matrix

D. Transport ATP from matrix to the cytoplasm

E. Transport phosphate back to the matrix

A

C

73
Q

Incubation of liver cells with both DNP and oligomycin will:

A. Blocks H+ pumping but enhances ATP synthesis

B. Enhances H+ pumping but blocks ATP synthesis

C. Blocks both H+ pumping and ATP synthesis

D. Enhances both H+ pumping and ATP synthesis

E. The effects of DNP and oligomycin cancel with each other and has no net effects

A

B

74
Q

T/F The surface of the inner mitochondrial membrane is large than that of outer.

A

True -cristae increases surface area

75
Q

How many ATP molecules are synthesized when the gamma subunit turns a full 360 degrees?

A

3

76
Q

How many ATP molecules are synthesized when one proton flows from the inter membrane space to the matrix?

A

1/4

  • 4 protons produces 1 ATP
  • 1 proton produces 1/4 ATP
77
Q

What is the driving force for adenosine translocase to move ATP into the inter membrane space and ADP into the matrix? phosphate translocase?

A
  • Electro potential- difference in charge
  • chemical potential- no difference in charge
78
Q

Why bother to go through the electron transport system in stead of oxidizing NADH/FADH2 by oxygen directly?

A

think

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