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Biochemistry > Week 7 - Unit 2 > Flashcards

Week 7 - Unit 2 Flashcards

1
Q

What type of bond is energy with ATP stored in?

A

Phosphoanhydride bonds

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2
Q

Phase 1 of respiration is the ______ of fuels. Phase 2 of respiration is _____ ______ from oxidative phosphorylation.

A

Oxidation

ATP generation

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3
Q

What 3 sources can ATP come from through respiration into the TCA cycle ?

A

Glucose
Fatty acids
Amino Acids

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4
Q

What three types of work is ATP used for ?

A 
Mechanical work (conformational changes)
Transport work (ATPases - Na/K transporter)
Biochemical work (energy of reactions)
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5
Q

To use the energy from ATP we ____ the reaction of the ____ of the P from ATP with another reaction that is less energetically favorable.

A

couple

cleavage

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6
Q

Delta G “not” in free energy standard conditions is favorable and unfavorable when ? (pH is 7.0 and 25 degrees C)

A

”-“ is a favorable reaction (exergonic)

“+” is an unfavorable reaction (endergonic)

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7
Q

Why is Delta G “not” not useful in real biological conditions ?

A

Its outcome is not altered by a change in substrate concentration

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8
Q

When the ratio of product to substrate = 1 (Keq = 1) then what is the Delta G “not”?

A

Zero

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9
Q

When Keq is greater than 1 (product is greater than substrate ) then what is the Delta G “not” ?

A

Less than zero - favorable

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10
Q

When Keq is less than 1, ( product is less than substrate), then what is the delta G “not” ?

A

Greater than zero, unfavorable

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11
Q

What does Delta G do differently versus its “not” version?

A
  • considers concentrations of products or substrates
  • takes into consideration of driving forces toward equilibrium
  • tells you how fare the reactions shifted to the right or left to reach equilibrium (Keq)
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12
Q

Although cellular temp and pH is not far from the standard (7.0 pH and 25 C), the ___ , ____, and ___ are very different from the standard 1M concentrations.

A

ATP
ADP
Pi
(concentrations)

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13
Q

Values can be ____ such that endergonic and exergonic reactions are coupled so that the overall Delta G is _____.

A

additive

negative

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14
Q

What does phosphoglucomutase do ?

A

Conversion of Glucose 6-phosphate (G6-P) to G1-P

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15
Q

What is the Delta G “not” of the reaction for converting G6-P to G1-P in standard conditions ?

A

1.65 (unfavorable)

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16
Q

how do we make in biological conditions the G6-P to G1-P from unfavorable to favorable?

A

Reduce the amount of product (constantly removed from system in metabolism)

  • decrease the ratio of product to substrate
  • makes the Delta G to negative overall and more favorable
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17
Q

True or False:
The delta G “not” is a description of the magnitude of the shift in one direction or another to reach equilibrium at any concentration.

A

False - “any” is key work, Delta G “not” can only calculate at standard conditions, not at “any” conditions

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18
Q

True or False:

A reaction can become favorable if the ratio of P/S becomes low enough

A

True- driving force to equilibrium

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19
Q

True or False:

The Delta G NOT for the forward and the reverse of a reaction is the same.

A

False- they are opposite

If forward = -2 then the reverse will be +2

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20
Q

What is reduced in the TCA cycle then Oxidized in ETS for use to make ATP?

A

NAD (H)

FAD (H2)

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21
Q

True or False:

In the ETS a Membrane potential and a pH potential exists between the Mitochondrial membranes

A

True

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22
Q

What is the only complex in ETS that is not transmembrane ?

A

Complex 2

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23
Q

What portion of the pathway in ETS is considered oxidative portion ?

A

Complex 1 through 4

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24
Q

What portion of ETS is considered substrate level phosphorylation ?

A

ATP Synthase (Complex 5)

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25
Q

What are the three ways to oxidize compounds ?

A
  1. Transfer of electrons from the compound as a hydrogen or Hydride
  2. Direct addition of oxygen
  3. Direct donation of electrons
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26
Q

What type of compounds are NAD and FAD ?

A

Co-enzymes

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27
Q

NAD+ is involved in the oxidation of _____ or _____.

A

Alcohols

Aldehydes

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28
Q

NAD+ will accept _____ as a hydride ion on its ______ ring in one location.

A

2 electrons from a Alcohol or Aldehyde

Nicotinamide

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29
Q

NAD+ can release a _____ into the medium.

A

Proton

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30
Q

FAD is involved in the formation of ____ bonds. It accepts _____ as hydrogen atoms separately.

A

double bonds

2 Electrons (opposite sides of rings on Riboflavin molecule)

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31
Q

Delta E NOT is a value that quantifies ?

The more negative the value…..

A

The energy change when a compound becomes reduced.

The more energy to make ATP

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32
Q

Who has the more negative Delta E NOT , NADH or FADH2 ?

A

NADH is more negative (more energy to make- 3 ATP)

FADH2 (only makes 2 ATP)

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33
Q

Where does the energy that NAD and FAD get in reduction come from ?

A

oxidation of food from breaking C-C and C-H bonds

glucose, palmitate

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34
Q

What are the features of the Cytosolic side of Mitochondria in the ETS?

A

Slightly more acidic, more H+
More positively charged
-Inner space between two membranes that Protons are pumped into to create gradient

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35
Q

What are the features of the Matrix side of the Mitochondria in the ETS?

A

less acidic than the Cytosolic side
less H+ (more negative than Cytosolic side)
-inner part of Mitochondria

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36
Q

What comprises Complex 1 in ETS ?

A

NADH
CoQ oxidoreductase
Binding side for Flavin mononucleotide
Iron-Sulfur center

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37
Q

What are the first steps of ETS involving Complex 1?

A
  1. Electrons from NADH will be passed to Flavin Mononucleotide
  2. Then passed 2 electrons to iron-sulfur center within the protein Complex 1 and reaction is coupled with sending 4 protons into Intermembrane space
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38
Q

Iron-sulfur center in Complex 1 (NADH:CoQ oxidoreductase) will transfer the 2 electrons it is holding to ?

A

Coenzyme Q (coQ)

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39
Q

CoQ can accept electrons from ?

A

Complex 1 and Complex 2 (free to move around, not bound to membrane)

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40
Q

CoQ in the fully oxidized form is called ?

A

Quinone form

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41
Q

When CoQ accepts a single Electron and Proton it is called ? stable or unstable?

A

Semiquinone form
(free radical)
Very unstable

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42
Q

When CoQ accepts 2 Electrons and 2 protons after its Semiquinone form (free radical), what is it called ?

A

Fully reduced form =

Dihydroquinol , (QH2)

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43
Q

After NADH oxidoreductase (Complex 1) transfers electrons to CoQ and has moved 4 electrons into intermembrane space, what happens next?

A
  1. Electrons from CoQ can be transferred to Complex III (or Cytochrom b-c1)
  2. Complex III will use Heme-Fe complex to transfer electrons (Fe3+ reduced to Fe2+ as electrons move down chain)
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44
Q

In the heme-Fe prosthetic groups in the enzymes of Cytochrome bc-1 (complex 3), differ slightly as to allow for ?

A

Redox potential is maintained as the electrons are transported down each protein

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45
Q

What is the last complex before the ATP synthase ?

A

Complex 4 - cytochrome oxidase

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46
Q

What does the cytochrome oxidase (complex 4- Cytochrome C) do ?

A

Transfers 4 electrons to oxygen using a Copper ion

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47
Q

What is Complex II called ? what does it bind as opposed to Complex 1?

A 
Succinate Dehydrogenase (also part of TCA cycle)
Binds FADH (complex 1 binds NADH)
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48
Q

True or false:

Complex II succinate Dehydrogenase can pump protons into the intermembrane space.

A

False - it is not transmembrane, and is the only complex that can not pump protons into intermembrane space

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49
Q

In the oxidation of FADH, the electrons are transferred where in Complex II (succinate dehydrogenase) ?

A

Iron-sulfur center and then to CoQ to make CoQH2

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50
Q

What comprises the F1 (headpiece) of the ATP Synthase (complex V)

A

Head unit = 3 dimers of alpha-beta chains

  • head held stationary by gamma and epsilon subunit
  • stabilized by long Delta chain on side
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51
Q

What comprises the F0 (pore) subunit of ATP synthase ?

A

12 monomeric C proteins (numbered)
-each has a portion open to cytoplasmic side that can be opened to matrix side during turning - allows movement of protons back into matrix during turning

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52
Q

Positive protons will attach to _____ _____ group in the C subunit (F0- pore side). C subunit will then rotate towards matrix side and release the proton from group.

A

Glutamyl carboxyl

53
Q

Rotation by the C monomeric proteins is due to the attraction between the Glutamyl carboxyl group on the C proteins and ______ charged ______ group on A subunit.

A

Positively

arginyl

54
Q

Turning of the F0 core proteins is coupled with ___ generation by the F1 headpiece.

A

ATP

55
Q

The gamma stock is penetrating the Headpiece of the Alpha-Beta dimers , as the stock turns, it will ?

A

point to one of the three pairs of units in the head piece

56
Q

When ADP and free Pi is bound to the headpiece, after the free proton passes through A subunit , the _____ will turn and facilitate a conformation change in the A-B head units. This will facilitate the synthesis of ____. Then release it and leave site open again for ADP and free phosphate .

A

Gamma stock

ATP

57
Q

The oxidized form of Coenzyme Q is considered a _____ while the fully reduced form is considered a _____.

A

Quinone

Dihydroquinol

58
Q

What can Coenzyme Q carry in its fully reduced form?

A

2 Electrons

2 Protons

59
Q

What two things are critical for the creation of ATP?

A
  1. Proton Gradient
  2. Membrane potential - limited permeability
  3. Anti-port to export ATP and import ADP
60
Q

How does ADP and the free phosphate get into the mitochondria for creation of ATP?

A
  1. Anti-port for ADP to enter vs ATP exits

2. Symport for Free phosphate + Hydrogen (H+) to enter

61
Q

What is the purpose of the Malate aspartate shuttle?

A
  1. shuttle the Hydrogen from NADH outside mitochondria across the membrane to NAD+ on the interior and reduces it to NADH
    (NADH can not cross membrane
62
Q

What does NADH give its electrons to outside the mitochondria to shuttle into the mitochondria ?

A
  1. Oxaloacetate takes the electrons and is reduced to Malate in the Cytosol
63
Q

What does the malate (oxaloacetate reduced to this) do once in the mitochondria?

A
  1. NAD+ inside the mitochondria is reduced to NADH

2. Malate is oxidized back to Oxaloacetate

64
Q

How does Malate Aspartate shuttle pathway get the Malate back outside the mitochondria after it is reduced back to Oxaloacetate?

A
  1. Transamination of Oxaloacetate to Aspartate using Glutamate
  2. Glutamate is turned into an alpha-keto acid (a-KG)
  3. Aspartate is now able to use antiport paired with Glutamate entering to exit mitochondria
65
Q

What is the purpose of the Glycerol 3-Phosphate shuttle?

A

NADH is used to reduce Dihydroxyacetone-P to Glycerol 3-Phosphate that can pass through Mitochondrial membrane that can then pass its H to FAD

66
Q

Who does Glycerol 3-P donate its electrons to once inside the mitochondria ?

A

FAD to make it FAD (2H) for use in the ETS

67
Q

What are the two shuttle systems used to get the electrons across Mitochondrial membrane (NADH) to give to NAD+ and FAD inside mitochondria to give to ETS system?

A

Malate Aspartate shuttle pathway

Glycerol 3-Phosphate pathway

68
Q

What is the previous form of Glycerol 3-P before it was reduced by NADH?

A

Dihydroxyacetone-P

69
Q

Coupling of the transfer of electrons must be coupled with the transfer of _____ in the ETS system - function fulfilled by CoQ. This determines ______….

A

Protons

How fast oxygen is going to be consumed

70
Q

What does an Inhibitor do to disrupt the ETS?

A

BLOCKS transport chain = no ATP generation

  • no Oxygen consumption
  • stop passing of electrons from subunit to subunit
71
Q

What does an Uncoupler do to disrupt the ETS?

A

DISIPATES the proton gradient = no ATP generation

  • electrons still passed and accepted by Oxygen
  • Increased Oxygen consumption
72
Q

What inhibits transfer of electrons from Complex 1 to CoQ ?

A

Rotenone

Amytal

73
Q

What inhibits transfer of electrons from Complex III to cytochrome C ?

A

Antimycin C

74
Q

What inhibits transfer of electrons from complex 4 to oxygen ?

A 
Carbon Monoxide (CO) 
Cyanide (CN)
75
Q

What inhibits the adenine nucleotide translocase (ANT)?

A

Atractyloside

76
Q

What inhibits the proton flow through the F0 component of the ATP synthase ?

A

Oligomycin

77
Q

What is an uncoupler, that facilitates proton transfer across the inner mitochondrial membrane?

A

Dinitrophenol

78
Q

What is an uncoupler that is a potassium ionophore, that facilitates potassium ion transfer across the inner mitochondria membrane ?

A

Valinomycin

79
Q

What are the two uncouplers ?

A

Dinitrophenol

Valinomycin

80
Q

What is the biological example of an uncoupler ?

A

Brown fat - thermoregulatory proteins - shivering and generation of heat

81
Q

In brown fat example of a biological uncoulper (passes electrons and uses Oxygen but makes no ATP- membrane was disrupted), what is the name of the protein that is in the membrane that allows transport of Protons from intermembrane space back into the matrix?

A

Thermogenin

82
Q

What does Thermogenin do?

A

Allows the Protons back into the Matrix preventing a proton gradient
-heat is created (shivering) as energy is lost as heat since it can not be transferred to make ATP

83
Q

The addition of rotenone to a biological system would?

A

(inhibitor of electrons transported)
Decrease the rate of oxygen consumption - reduces the number of electrons avaliable by inhibiting Complex 1 - reduces the production of water hence less oxygen used

84
Q

How does Dinitrophenol (DNP) effect the mitochondrial organelle?

A
  • impacts membrane
    -exchanges protons between matrix and inter-membrane space- dissipating gradient
    (uncoupler- will only effect protons, but electrons can still consume oxygen)
85
Q

Mitochondria disorders are due to mutation in _____ or _______

A

nDNA or mtDNA

86
Q

mtDNA is circular and ____ in nature. It is only passed from ____ to child.

A

Maternal

mother

87
Q

Phenotype for Mitochondrial disease presentation is variable due to _______: due to random segregation of the mitochondrion.

A

Heteroplasmy

88
Q

Evaluate mitochondrial genetic disorders by evaluating changes in _____.

A

mtDNA (not able to repair DNA and replicates independently of nDNA)

89
Q

Heteroplasmy - mother may contribute two different populations - mutant and normal - and then during replication they will segregate randomly so that :

A

Some cells get more mutant mitochondria than others during development
-Replication of Mitochondria is controlled by amount of ATP (independent)

90
Q

Phenotype is usually displayed in high energy tissues such as ______ and the ______. So that they will present with muscle _____ and ______ symptoms

A

Skeletal muscle

Brain

Weakness

Neurological

91
Q

Quantify the amount of mutant mitochondria in a cell through ______ ______.

A

restriction mapping - can track heritable mutation

92
Q

If a male presents with symptoms characteristic of an mtDNA disorder, what is the likelihood that his children will also present with the disease?

A

0%- mtDNA defects are only passed through the mother

93
Q

Complex _____ aka ______ is not required for oxidative phosphorylation because it does not span the mitochondrial membrane. It accepts which coenzyme?

A

Complex II
FADH/succinate dehydrogenase

FAD(H2)

94
Q

Complex 1 is aka?

A

NADH dehydrogenase

95
Q

CoQ is aka?

A

Quinone derivative

96
Q

Complex II is aka?

A

FADH/succinate dehydrogenase

97
Q

Complex III is aka?

A

Cytochrome c and b

98
Q

Complex IV is aka ?

A

Cytochrome c, a and a3

99
Q

Complex V is aka?

A

ATP synthase

100
Q

Uncouplers disrupt the mitochondrial membrane and reduce ATP product and ____ oxygen consumption.

A

Increase

101
Q

NADH or FADH2 generated in the cytosol of cell must be ____ _____ into the mitochondria.

A

transported actively

102
Q

Succinate is a substrate for which complex in the ETS?

A

Complex 2- coupled to TCA cycle and accepts succinate rather than malate as substrate

103
Q

Mechanical work is best described as ?

A

conversion of a high energy bond to instigate a conformational change in a protein

104
Q

In the case of an exothermic reaction, what would Delta G NOT be ?

A

Negative - indicative of a spontaneous reaction

105
Q

What is Delta S described as ?

A

change in entropy or an increase in disorder and this value is often negligible in reactions

106
Q

The last cytochrome in the ETC, cytochrome oxidase, passes electrons to O2. Cytochrome oxidase is able to do this because ….

A

it has lower Km for oxygen then hemoglobin

107
Q

Lower Km for oxygen allows ______ _____ to ‘pull’ oxygen from myoglobin and hemoglobin, additionally is is bound to copper ions that allows for the collection of 4 electrons required for the reduction of _____.

A

Cytochrome oxidase

oxygen

108
Q

Fuel oxidation is _____: It releases energy. It has a _____ value for Delta G NOT. This means the products have a lower chemical bond energy than the reactants and their formation is energetically favored.

A

exergonic

negative

109
Q

What is Delta H ?

A

Change in enthalpy- measurement of total heat content

-equal to the internal energy of system

110
Q

What is Delta S ?

A

Change in entropy , or increase in disorder

111
Q

What is an example of biochemical work ?

A

Anabolic pathways - synthesis of DNA, glycogen, proteins)

112
Q

What is an example of Transport work ?

A

(active transport)- ATP used to move compounds against gradient
-Na+/K+ pump ATPase

113
Q

What is an example of Mechanical work ?

A

high energy bond is converted into movement by changing conformation of protein

  • contracting muscle fibers
  • motor proteins that transport chemicals along fibers
114
Q

What does NADPH stand for ?

A

Nicotinamide adenine dinucleotide phosphate

115
Q

What does FAD stand for ?

A

Flavin adenine dinucleotide

116
Q

True or False:

NAD and NADP have the same reduction potential

A

True

117
Q

The more ______ a reduction potential of a compound, the greater is the energy avaliable for ATP generation.
NADH has a more _____ potential than FAD.

A

negative

negative

118
Q

NADPH has and extra phosphate group on the ____, which affects its enzyme binding so usually either NADPH is used or NAD not both. It is usually used in energy-requiring reactions without first being converted to ____ currency.

A

Ribose

ATP

119
Q

What is the reducing agent?

A

The element or compound that loses or “donates” an electron to another compound
(the reducing agent is the one that gets oxidized)

120
Q

What is the oxidizing agent?

A

The compound that gains or accepts electrons and hence oxidizes another compound
(the oxidizing agent is the one that gets reduced)

121
Q

Can ADP, ATP, phosphate, pyruvate , and other metabolites move freely across the Inner mitochondria membrane ?

A

no- they must be transported through inner and outer membranes

122
Q

What is able to make it through the outer membrane that is more permeable in the mitochondria ?

A

Anions up to 6000Da due to large nonspecific pores in outer membrane

  • phosphate, chloride, pyruvate , citrate , adenine nucleotides
  • several kinases make it through to bind the ATP being transported out
123
Q

A lack of ATP for maintaining low intracellular ___ can lead to pore opening, and then protons flood in and maintaining a gradient becomes almost impossible to make more ATP. Leads to necrosis , lysis

A

Ca+

124
Q

In a temporary lack of Oxygen (O2), the ATP synthase will do what?

A

Run backwards and hydrolyze the ATP back into ADP +P to try to maintain equilibrium

125
Q

What is DHAP , where is it found?

A

Dihydroxyacetone-P

  • in the Glycerol 3-phosphate shuttle pathway
  • it is the reactant outside the MT that will be reduced by NADH to make Glycerol 3-P that crosses the MT to reduce FAD
126
Q

FAD in the mitochondria is contained in what (relative to Glycerol 3-phosphate shuttle)

A

FAD is contained in glycerol phosphate dehydrogenase

127
Q

A series of reactions have the following Delta G:
A+B —-> C Delta G = -
C+D —-> E Delta G = +3
E+F —-> G Delta G = -5
What is the overall Delta G for this series of reactions

A

-3

The Delta G for a series of reactions is additive

128
Q

The fully reduced quinol form of CoQ contains what combination of electrons and protons

A

2 electrons and 2 protons

Biochemistry (20 decks)

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