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PLE 2014: Biochem by kachMD > Bioenergetics > Flashcards

Bioenergetics Flashcards

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1
Q

What is the transfer and utilisation of energy in biologic systems?

A

Bioenergetics

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2
Q

What is Bioenergetics?

A

Bioenergetics is the transfer and utilisation of energy in biologic systems

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3
Q

What is the measure of the heat content of the reactants and products?

A

Enthalpy (ΔH)

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4
Q

What is the measure of the change in randomness or disorder of the reactants and products?

A

Entropy (ΔS)

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5
Q

What is Enthalpy (ΔH)? Unit of measurement?

A

Enthalpy (ΔH) is the measure of the heat content of the reactants and products. It is measured in joules (J)

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6
Q

What is Entropy (ΔS)? Unit of measurement?

A

Entropy (ΔS) is the change in randomness or disorder of the reactants and products. It is measured in joules/kelvin (J/K)

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7
Q

What predicts the direction in which a reaction will spontaneously proceed?

A

Change in Free Energy (ΔG)

ΔG = ΔH - [T in kelvin * (ΔS)]

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8
Q

What is ΔG when a reaction proceeds to equilibrium?

A

ΔG approaches zero

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9
Q

What is the measure of energy available to do work?

A

Change in Free Energy (ΔG)

ΔG = ΔH - (T in kelvin) (ΔS)

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10
Q

What is change in Free Energy (ΔG)?

A

Change in Free Energy (ΔG) is the measure of energy available to do work. It predicts the direction in which a reaction will spontaneously proceed or if a reaction is favourable.

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11
Q

What predicts if a reaction is favourable or not? What value will favor a spontaneous reaction?

A

Change in Free Energy (ΔG) A negative ΔG will favor a spontaneous reaction.

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12
Q

What is difference of enthalpy and the product of entropy and absolute temperature?

A

Change in Free Energy (ΔG)

ΔG = ΔH - (T in kelvin) (ΔS)

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13
Q

What is standard free energy change? What are the conditions?

A

Standard free energy change is ΔG under standard conditions. 1) reactants and products are 1 molar each 2) temp is 25°C or 298K 3) pressure is 1 atm

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14
Q

Apart from Change in Free Energy (ΔG), what else can be used to predict whether a reaction is spontaneous or not?

A

NONE. Only ΔG can be used to predict whether a reaction is spontaneous or not.

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15
Q

If ΔG < 0, what is the net energy of the products compared to the reactants? Is it spontaneous?

A

If ΔG < 0 or negative ΔG, there is a net loss of energy or it is EXERGONIC hence it is spontaneous.

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16
Q

If ΔG > 0, what is the net energy of the products compared to the reactants?

A

If ΔG > 0 or positive ΔG, there is a net gain of energy or it is ENDERGONIC hence it is not spontaneous.

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17
Q

If ΔG = 0, what is the net energy of the products compared to the reactants?

A

If ΔG = 0, the energy is the same or it is in EQUILIBRIUM hence the forward and backward reactions are equal.

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18
Q

What value of ΔG will favor a spontaneous reaction?

A

A negative ΔG will favor a spontaneous reaction.

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19
Q

Differentiate endERGONIC & exERGONIC vs. endoTHERMIC & exoTHERMIC.

A

endERGONIC & exERGONIC = free energy

“GO and be FREE”

endoTHERMIC & exoTHERMIC = heat content

“_THERM_ometers measure _HEAT CONTENT_”

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20
Q

Is a reaction spontaneous if:

Enthalpy = negative

Entropy = positive

A

YES, it is ALWAYS spontaneous

ΔG = ΔH - [T * (ΔS)]

Enthalpy (ΔH) = negative

Entropy (ΔS) = positive

***you will always get a negative value if you subtract a positive value from a negative number

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21
Q

Is a reaction spontaneous if:

Enthalpy = negative

Entropy = negative

A

It MAY BE spontaneous but only at LOW TEMP

ΔG = ΔH - [T * (ΔS)]

Enthalpy (ΔH) = negative

Entropy (ΔS) = positive

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22
Q

Is a reaction spontaneous if:

Enthalpy = positive

Entropy = negative

A

NO, it is NEVER spontaneous

ΔG = ΔH - [T * (ΔS)]

Enthalpy (ΔH) = positive

Entropy (ΔS) = negative

***you will always get a positive value if you subtract a negative value from a positive number (double negatives become addition)

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23
Q

Is a reaction spontaneous if:

Enthalpy = positive

Entropy = positive

A

It MAY BE spontaneous but only at HIGH TEMP

ΔG = ΔH - [T * (ΔS)]

Enthalpy (ΔH) = positive

Entropy (ΔS) = positive

***to yield a negative ΔG, [ΔS*T] which can be achieved with a HIGH temp

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24
Q

What are coupling reactions for?

A

Large negative ΔG reactions couple with a smaller positive ΔG reactions to yield an overall negative ΔG.

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25
True of False: All ΔG's of a pathway are additive.
True. All ΔG's of a pathway are additive. The ΔG° of 2 consecutive reactions are additive.
26
True of False: Coupled processes can occur spontaneously if the reaction has a net positive ΔG.
False. Energetically coupled processes can occur spontaneously if the reaction has a net NEGATIVE ΔG.
27
What is an adenosine molecule to which 3 phosphate groups are attached?
Adenosine Triphosphate (ATP)
28
What is the function of ATP?
ATP acts as the "Energy currency" of the cell, transferring free energy derived from substance of higher energy potential to those of lower potential.
29
What is the ΔG° of the hydrolysis of 1 phosphate from ATP? from ADP?
ATP → ADP + Pi **ΔG° = -7,300 cal/mol** ADP → AMP + Pi **ΔG° = -6,600 cal/mol**
30
What can be used to make ATP? Examples?
Any ΔG° \> ATP can be used to make ATP Ex. PEP, creatine phosphate, carbamoyl phosphate, etc (see pg. 5 topnotch handouts)
31
What acts as the "Energy currency" of the cell?
ATP acts as the "Energy currency" of the cell by transferring free energy derived from substance of higher energy potential to those of lower potential.
32
What are the sources of high energy phosphate?
1. Oxidative Phosphorylation 2. Substrate Level Phosphorylation
33
What is the greatest quantitative source of high energy phosphate in aerobic organisms?
Oxidative Phosphorylation
34
In oxidative phosphorylation, what is the final substance to be reduced?
molecular oxygen
35
What is done through coupling reactions where a phosphate is transferred to ADP from another substance with higher ΔG°?
Substrate Level Phosphorylation
36
free energy comes from a successive oxidation of substances in the respiratory chain within the mitochondria
Oxidative Phosphorylation
37
What is Oxidative Phosphorylation?
Oxidative Phosphorylation is where free energy comes from a successive oxidation of substances in the respiratory chain within the mitochondria.
38
What is Substrate Level Phosphorylation?
Substrate Level Phosphorylation is done through coupling reactions where a phosphate is transferred to ADP from another substance with higher ΔG°.
39
In a oxidation-reduction reaction, which reaction loses electrons?
Oxidation loses electrons. "l**_O_**se the **_O_** in **_O_**xidation"
40
In a oxidation-reduction reaction, which reaction gains electrons?
Reduction gains electrons. "gain the **_E_** in r**_E_**duction"
41
True or False: Oxidation and Reduction are 2 separate reactions.
False. Oxidation and Reduction ALWAYS go together. If something loses an electron (oxidised) something else gains the electrons (reduced).
42
How many reactions (steps) in glycolysis will generate ATP?
ATP is generated in 2 steps. 1,3-BPG + ADP → 3-PG + ATP (phosphoglycerate kinase) PEP + ADP → pyruate + ATP (pyruvate kinase) *"**AT**e, **P**abukas ng **GATE** **K**apag **P**apasok si **K**uya"* ***AT**P: **P**hospho**g**lycer**ate** **K**inase, **P**yruvate **K**inase*
43
How many reactions (steps) in the TCA cycle will generate ATP?
ATP is generated in 1 step. Succinyl-CoA + ADP → Succinate + ATP (enzyme: **succinyl thiokinase**)
44
What is the final common pathway by which electrons from the different fuels of the body flow to oxygen?
The Electron Transport Chain (ETC) is the final common pathway by which electrons from the different fuels of the body flow to oxygen
45
What are the two carriers used in the ETC?
1. Nicotinamide Adenine Dinucleotide (NAD) 2. Flavin Adenine Dinucleotide (FAD)
46
Where does the ETC occur?
The ETC take place in the inner mitochondrial membrane.
47
What is the ETC?
The Electron Transport Chain (ETC) is the final common pathway by which electrons from the different fuels of the body flow to oxygen
48
What vitamin is NAD derived from?
NAD is derived from NIACIN (vitamin B3)
49
What vitamin is FAD derived from?
FAD is derived from RIBOFLAVIN (vitamin B2)
50
Which mitochondrial membrane is freely permeable to most molecules?
The OUTER mitochondrial membrane is freely permeable to most molecules.
51
Which mitochondrial membrane is impermeable to most molecules?
The INNER mitochondrial membrane is impermeable to most molecules.
52
What is the function of the cristae of the mitochondria?
The cristae of the mitochondria increases surface area.
53
What can be found in the mitochondrial matrix?
The mitochondrial matrix contains enzymes, mtDNA, mtRNA, ribosomes.
54
What is formed when NAD and FAD receive electrons from other substances? What happens next?
NADH and FADH2 are formed and donate electrons to specialised set of carrier in the ETC.
55
In which part of ETC is NADH dehydrogenase found?
Complex I: NADH dehydrogenase
56
In which part of ETC is Succinate dehydrogenase found?
Complex II: Succinate dehydrogenase
57
In what part of ETC is ubiquinone found?
Coenzyme Q: Ubiquinone \*only non-protein part of the ETC
58
In what part of ETC is Cytochrome b/c1 found?
Complex III: Cytochrome b/c1 or Ferricytochrome oxidoreductase
59
In what part of ETC is Fe/heme protein found?
Cytochrome C: Fe/heme protein \*the mobile part of the ETC
60
In what part of ETC is Cytochrome a/a3 found?
Complex IV: Cytochrome a/a3 (Cu/heme protein) \*aka Cytochrome oxidase
61
What is in Complex I of the ETC?
Complex I: NADH dehydrogenase
62
What is in Complex II of the ETC?
Complex II: Succinate dehydrogenase
63
What is in Complex III of the ETC?
Complex III: Cytochrome b/c1 or Ferricytochrome oxidoreductase
64
What is in Complex IV of the ETC?
Complex IV: Cytochrome a/a3 (Cu/heme protein) \*aka Cytochrome oxidase
65
What is in Coenzyme Q of the ETC?
Coenzyme Q: Ubiquinone \*only non-protein part of the ETC
66
What is in Cytochrome C of the ETC?
Cytochrome C: Fe/heme protein \*the mobile part of the ETC
67
What in the only non-protein part of the ETC?
Coenzyme Q / Ubiquinone is the only non-protein part of the ETC.
68
What is the mobile part of the ETC?
Cytochrome C: Fe/heme protein is the mobile part of the ETC
69
Which complexes in the ETC are parallel?
Complexes I & II
70
Which complex does NADH bind to?
Complex I: NADH dehydrogenase
71
Which complex does FADH2 bind to?
Complex II: Succinate dehydrogenase
72
Which complexes pump out protons to the inter membranous space to create a gradient?
1. Complex I: NADH dehydrogenase 2. Complex III: Cytochrome b & c1 3. Complex IV: Cytochrome c & a/a3
73
All components of the ETC are fixed to the inner mitochondrial membrane except which 2?
1. Coenzyme Q: Ubiquinone 2. Cytochrome C
74
What is the final electron acceptor in the ETC?
Oxygen is the final electron acceptor in the ETC.
75
What is MItchell's Chemiosmotic Theory?
Energy from the oxidation of components in the respiratory chain is coupled to the translocation of hydrogen ions from the inside to the outside of the inner mitochondrial membrane and accumulates in the inter membranous space. The proton gradient across the inner membrane is the driving force used by Oxidative phosphorylation to generate ATP.
76
What results in the synthesis of ATP in Oxidative Phosphorylation?
Protons driven to the mitochondrial matrix through a channel in Complex V / ATP synthase Complex results in the synthesis of ATP.
77
What type of gradient is created by the ETC? Across which mitochondrial membrane?
The ETC create an electrical and pH gradient across the inner mitochondrial membrane.
78
In which mitochondrial compartment is the gradient created? What are the components?
The intermembranous space is the compartment of greater concentration and is more positive and has more H+ ions.
79
What theory states that the ETC creates a proton gradient across the innermitochondrial membrane and that proton gradient is the driving force used by Oxidative Phosphorylation to generate ATP?
Mitchell's Chemiosmotic Theory
80
What are the 2 components of Complex V / ATP synthase Complex?
F1 generates ATP from ADP and Pi F0 is a channel where protons pass through
81
What deprives the ETC of sufficient oxygen, decreasing the rate of ETC and ATP production?
Tissue Hypoxia
82
What occurs in the mitochondria only?
Oxidative Phosphorylation
83
What occurs in BOTH cytoplasm and mitochondria?
Substrate Level Phosphorylation
84
What is in the F1 component of Complex V? What does it do?
F1 generates ATP from ADP and Pi
85
What is in the F0 component of Complex V? What does it do?
F0 is a channel where protons pass through
86
What is the effect of oxygen deprivation on the rate of ETC & ATP production?
Deprivation of the ETC of sufficient oxygen, **decreases** the rate of ETC and ATP production.
87
What is this? What is it for? Explain.
The **electron transport chain** is a network of electron-carrying proteins located in the inner mitochondrial membrane. These proteins transfer electrons from one to another, down the chain while pumping out H+ ions to the intermitochondril matrix. These electrons will eventually be added, along with protons, to oxygen, which is the final electron acceptor. This produces water, but does not produce any ATP. The ATP is actually produced by the influx of H+ ion due to its gradient force. This force is a store of potential energy created by the gradient formed when hydrogens (protons) are moved across a biological membrane. Therefore, the electron transport chain merely produces a gradient through which ATP can be made (this is known as chemiosmosis).
88
True or False: Anaerobic glycolysis is enough for highly aerobic tissues like the BRAIN and CARDIAC MUSCLES.
False. Anaerobic glycolysis is **NOT **enough for highly aerobic tissues like the BRAIN and CARDIAC MUSCLES.
89
Differentiate **INHIBITORS** from **UNCOUPLERS** of the ETC.
**INHIBITORS** stop the electron flow from substrate to oxygen hence no H+ gradient is created and no ATP is production. NADH and FADH2 accumulate. **UNCOUPLERS** increase the permeability of the inner mitochondrial membrane to protons losing the the H+ gradient needed to produce ATP but ETC still continues so there is no accumulation of NADH and FADH2.
90
What is Complex I? What are its inhibitors?
Complex I: NADH Dehydrogenase Inhibitors: Barbiturates, Piericidin A, Amytal, Rotenone
91
What is Complex II? What are its inhibitors?
Complex II: Succinate Dehydrogenase Inhibitors: Malonate, Carboxin, TTFA
92
What is Complex III? What are its inhibitors?
Complex III: Ubiquinol:Ferricytochrome oxidoreductase Inhibitors: Antimycin A, Dimercaprol
93
What is Complex IV? What are its inhibitors?
Complex IV: Cytochrome oxidase Inhibitors: Cyanide, Carbon monoxide, Sodium Azide, Hydrogen Sulfide
94
Give an example of a synthetic uncoupler of the ETC.
2,4 dinitrophenol Aspirin *NOTE: Aspirin OD manifests as hyperpyrexia due to the uncoupling of the ETC with increased body heat production*
95
Give an example of uncoupling proteins.
Thermogenin (brown fat) produce heat and prevent hypothermia in neonates
96
What are uncouplers?
Uncouplers increase the permeabily of the inner mitochondrial membrane to protons losing the gradient needed to produce ATP. However, ETC still continues and the substrate is still oxidized but the energy extracted from oxidation of substrates is dissipated as **HEAT.**
97
What are ATP Synthase Inhibitors? What are its effects?
ATP Synthase Inhibitors directly inhibit mitochondrial ATP synthase (Complex V). The proton gradient continues to rise but there is no "escape valve" for the protons so ETC eventually shuts down.
98
Give an example of an ATP synthase inhibitor.
**OLIGOMYCIN** directly inhibits Complex V.
99
What are unstable products that are formed as a byproduct of ETC when molecular O2 is partially reduced? Examples?
Reactive Oxygen Species 1. superoxide (O2-) 2. hydrogen peroxide (H2O2) 3. hydroxyl radical (OH-)
100
What are Reactive Oxygen Species?
Reactive oxygen species are unstable products that are formed as a byproduct of ETC when molecular O2 is partially reduced.
101
How to ROS fight against bacteria?
1. ROS react with lipids to cause peroxidation and disruption of cell membranes 2. ROS denatures and precipitates proteins and other substances
102
In the absence of anti-bacterial activity, when are ROS increased?
ROS are increased in reperfusion injury due to a sudden burst in ETC activity upon the introduction of O2
103
What are the defenses to ROS?
1. Catalase (vs. H2O2) 2. Peroxidase 3. Superoxide dimutase (vs. O2-)
104
What bacteria also produces catalase as a defense against H2O2?
Staphylococcus aureus
105
Are mitochondrial disease maternally or paternally inherited?
Mitochondrial diseases are maternally inherited.
106
What are mutations in the circular mitochondrial chromosome?
Mitochondrial Diseases
107
What is a mitochondrial disease affecting Complex I?
**Complex I: MELAS** Mitochondrial Encephalomyopathy Lactic Acidosis Stroke-like episodes
108
What is a mitochondrial disease affecting Complex II?
Complex II: **Kearns-Sayre Syndrome**
109
What is a mitochondrial disease affecting Complex III?
Complex III: **Leber's Hereditary Optic Neuropathy**
110
What is a mitochondrial disease affecting Complex IV?
Complex IV: **Leigh's Disease**
111
What is a mitochondrial disease affecting ALL complexes?
Fatal Infantile Mitochondrial Myopathy
112
Name the disease: * Progressive myoclonic epilepsy * Clumps of diseased mitochondria accumulate in muscle fibers and appear as "ragged-red fibers" when muscle is stained with modified Gömöri trichrome stain * Short stature
Myoclonic epilepsy and ragged-red fibers (MERRF)
113
Name the disease: * Varying degrees of cognitive impairment and dementia * Lactic acidosis * Strokes * Transient ischemic attacks * Hearing loss * Weight loss
Mitochondrial encephalomyopathy, lactic acidosis, and stroke-like syndrome (**MELAS**)
114
Name the disease: * External ophthalmoplegia * Cardiac conduction defects * Sensorineural hearing loss
Kearns-Sayre syndrome (KSS)
115
Name the disease: * Progressive ophthalmoparesis * Symptomatic overlap with other mitochondrial myopathies
Chronic progressive external ophthalmoplegia (CPEO)

PLE 2014: Biochem by kachMD (11 decks)

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