Week 7 - Unit 2 Flashcards
What type of bond is energy with ATP stored in?
Phosphoanhydride bonds
Phase 1 of respiration is the ______ of fuels. Phase 2 of respiration is _____ ______ from oxidative phosphorylation.
Oxidation
ATP generation
What 3 sources can ATP come from through respiration into the TCA cycle ?
Glucose
Fatty acids
Amino Acids
What three types of work is ATP used for ?
Mechanical work (conformational changes) Transport work (ATPases - Na/K transporter) Biochemical work (energy of reactions)
To use the energy from ATP we ____ the reaction of the ____ of the P from ATP with another reaction that is less energetically favorable.
couple
cleavage
Delta G “not” in free energy standard conditions is favorable and unfavorable when ? (pH is 7.0 and 25 degrees C)
”-“ is a favorable reaction (exergonic)
“+” is an unfavorable reaction (endergonic)
Why is Delta G “not” not useful in real biological conditions ?
Its outcome is not altered by a change in substrate concentration
When the ratio of product to substrate = 1 (Keq = 1) then what is the Delta G “not”?
Zero
When Keq is greater than 1 (product is greater than substrate ) then what is the Delta G “not” ?
Less than zero - favorable
When Keq is less than 1, ( product is less than substrate), then what is the delta G “not” ?
Greater than zero, unfavorable
What does Delta G do differently versus its “not” version?
- 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)
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.
ATP
ADP
Pi
(concentrations)
Values can be ____ such that endergonic and exergonic reactions are coupled so that the overall Delta G is _____.
additive
negative
What does phosphoglucomutase do ?
Conversion of Glucose 6-phosphate (G6-P) to G1-P
What is the Delta G “not” of the reaction for converting G6-P to G1-P in standard conditions ?
1.65 (unfavorable)
how do we make in biological conditions the G6-P to G1-P from unfavorable to favorable?
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
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.
False - “any” is key work, Delta G “not” can only calculate at standard conditions, not at “any” conditions
True or False:
A reaction can become favorable if the ratio of P/S becomes low enough
True- driving force to equilibrium
True or False:
The Delta G NOT for the forward and the reverse of a reaction is the same.
False- they are opposite
If forward = -2 then the reverse will be +2
What is reduced in the TCA cycle then Oxidized in ETS for use to make ATP?
NAD (H)
FAD (H2)
True or False:
In the ETS a Membrane potential and a pH potential exists between the Mitochondrial membranes
True
What is the only complex in ETS that is not transmembrane ?
Complex 2
What portion of the pathway in ETS is considered oxidative portion ?
Complex 1 through 4
What portion of ETS is considered substrate level phosphorylation ?
ATP Synthase (Complex 5)
What are the three ways to oxidize compounds ?
- Transfer of electrons from the compound as a hydrogen or Hydride
- Direct addition of oxygen
- Direct donation of electrons
What type of compounds are NAD and FAD ?
Co-enzymes
NAD+ is involved in the oxidation of _____ or _____.
Alcohols
Aldehydes
NAD+ will accept _____ as a hydride ion on its ______ ring in one location.
2 electrons from a Alcohol or Aldehyde
Nicotinamide
NAD+ can release a _____ into the medium.
Proton
FAD is involved in the formation of ____ bonds. It accepts _____ as hydrogen atoms separately.
double bonds
2 Electrons (opposite sides of rings on Riboflavin molecule)
Delta E NOT is a value that quantifies ?
The more negative the value…..
The energy change when a compound becomes reduced.
The more energy to make ATP
Who has the more negative Delta E NOT , NADH or FADH2 ?
NADH is more negative (more energy to make- 3 ATP)
FADH2 (only makes 2 ATP)
Where does the energy that NAD and FAD get in reduction come from ?
oxidation of food from breaking C-C and C-H bonds
glucose, palmitate
What are the features of the Cytosolic side of Mitochondria in the ETS?
Slightly more acidic, more H+
More positively charged
-Inner space between two membranes that Protons are pumped into to create gradient
What are the features of the Matrix side of the Mitochondria in the ETS?
less acidic than the Cytosolic side
less H+ (more negative than Cytosolic side)
-inner part of Mitochondria
What comprises Complex 1 in ETS ?
NADH
CoQ oxidoreductase
Binding side for Flavin mononucleotide
Iron-Sulfur center
What are the first steps of ETS involving Complex 1?
- Electrons from NADH will be passed to Flavin Mononucleotide
- Then passed 2 electrons to iron-sulfur center within the protein Complex 1 and reaction is coupled with sending 4 protons into Intermembrane space
Iron-sulfur center in Complex 1 (NADH:CoQ oxidoreductase) will transfer the 2 electrons it is holding to ?
Coenzyme Q (coQ)
CoQ can accept electrons from ?
Complex 1 and Complex 2 (free to move around, not bound to membrane)
CoQ in the fully oxidized form is called ?
Quinone form
When CoQ accepts a single Electron and Proton it is called ? stable or unstable?
Semiquinone form
(free radical)
Very unstable
When CoQ accepts 2 Electrons and 2 protons after its Semiquinone form (free radical), what is it called ?
Fully reduced form =
Dihydroquinol , (QH2)
After NADH oxidoreductase (Complex 1) transfers electrons to CoQ and has moved 4 electrons into intermembrane space, what happens next?
- Electrons from CoQ can be transferred to Complex III (or Cytochrom b-c1)
- Complex III will use Heme-Fe complex to transfer electrons (Fe3+ reduced to Fe2+ as electrons move down chain)
In the heme-Fe prosthetic groups in the enzymes of Cytochrome bc-1 (complex 3), differ slightly as to allow for ?
Redox potential is maintained as the electrons are transported down each protein
What is the last complex before the ATP synthase ?
Complex 4 - cytochrome oxidase
What does the cytochrome oxidase (complex 4- Cytochrome C) do ?
Transfers 4 electrons to oxygen using a Copper ion
What is Complex II called ? what does it bind as opposed to Complex 1?
Succinate Dehydrogenase (also part of TCA cycle) Binds FADH (complex 1 binds NADH)
True or false:
Complex II succinate Dehydrogenase can pump protons into the intermembrane space.
False - it is not transmembrane, and is the only complex that can not pump protons into intermembrane space
In the oxidation of FADH, the electrons are transferred where in Complex II (succinate dehydrogenase) ?
Iron-sulfur center and then to CoQ to make CoQH2
What comprises the F1 (headpiece) of the ATP Synthase (complex V)
Head unit = 3 dimers of alpha-beta chains
- head held stationary by gamma and epsilon subunit
- stabilized by long Delta chain on side
What comprises the F0 (pore) subunit of ATP synthase ?
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
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.
Glutamyl carboxyl
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.
Positively
arginyl
Turning of the F0 core proteins is coupled with ___ generation by the F1 headpiece.
ATP
The gamma stock is penetrating the Headpiece of the Alpha-Beta dimers , as the stock turns, it will ?
point to one of the three pairs of units in the head piece
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 .
Gamma stock
ATP
The oxidized form of Coenzyme Q is considered a _____ while the fully reduced form is considered a _____.
Quinone
Dihydroquinol
What can Coenzyme Q carry in its fully reduced form?
2 Electrons
2 Protons
What two things are critical for the creation of ATP?
- Proton Gradient
- Membrane potential - limited permeability
- Anti-port to export ATP and import ADP
How does ADP and the free phosphate get into the mitochondria for creation of ATP?
- Anti-port for ADP to enter vs ATP exits
2. Symport for Free phosphate + Hydrogen (H+) to enter
What is the purpose of the Malate aspartate shuttle?
- 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
What does NADH give its electrons to outside the mitochondria to shuttle into the mitochondria ?
- Oxaloacetate takes the electrons and is reduced to Malate in the Cytosol
What does the malate (oxaloacetate reduced to this) do once in the mitochondria?
- NAD+ inside the mitochondria is reduced to NADH
2. Malate is oxidized back to Oxaloacetate
How does Malate Aspartate shuttle pathway get the Malate back outside the mitochondria after it is reduced back to Oxaloacetate?
- Transamination of Oxaloacetate to Aspartate using Glutamate
- Glutamate is turned into an alpha-keto acid (a-KG)
- Aspartate is now able to use antiport paired with Glutamate entering to exit mitochondria
What is the purpose of the Glycerol 3-Phosphate shuttle?
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
Who does Glycerol 3-P donate its electrons to once inside the mitochondria ?
FAD to make it FAD (2H) for use in the ETS
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?
Malate Aspartate shuttle pathway
Glycerol 3-Phosphate pathway
What is the previous form of Glycerol 3-P before it was reduced by NADH?
Dihydroxyacetone-P
Coupling of the transfer of electrons must be coupled with the transfer of _____ in the ETS system - function fulfilled by CoQ. This determines ______….
Protons
How fast oxygen is going to be consumed
What does an Inhibitor do to disrupt the ETS?
BLOCKS transport chain = no ATP generation
- no Oxygen consumption
- stop passing of electrons from subunit to subunit
What does an Uncoupler do to disrupt the ETS?
DISIPATES the proton gradient = no ATP generation
- electrons still passed and accepted by Oxygen
- Increased Oxygen consumption
What inhibits transfer of electrons from Complex 1 to CoQ ?
Rotenone
Amytal
What inhibits transfer of electrons from Complex III to cytochrome C ?
Antimycin C
What inhibits transfer of electrons from complex 4 to oxygen ?
Carbon Monoxide (CO) Cyanide (CN)
What inhibits the adenine nucleotide translocase (ANT)?
Atractyloside
What inhibits the proton flow through the F0 component of the ATP synthase ?
Oligomycin
What is an uncoupler, that facilitates proton transfer across the inner mitochondrial membrane?
Dinitrophenol
What is an uncoupler that is a potassium ionophore, that facilitates potassium ion transfer across the inner mitochondria membrane ?
Valinomycin
What are the two uncouplers ?
Dinitrophenol
Valinomycin
What is the biological example of an uncoupler ?
Brown fat - thermoregulatory proteins - shivering and generation of heat
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?
Thermogenin
What does Thermogenin do?
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
The addition of rotenone to a biological system would?
(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
How does Dinitrophenol (DNP) effect the mitochondrial organelle?
- impacts membrane
-exchanges protons between matrix and inter-membrane space- dissipating gradient
(uncoupler- will only effect protons, but electrons can still consume oxygen)
Mitochondria disorders are due to mutation in _____ or _______
nDNA or mtDNA
mtDNA is circular and ____ in nature. It is only passed from ____ to child.
Maternal
mother
Phenotype for Mitochondrial disease presentation is variable due to _______: due to random segregation of the mitochondrion.
Heteroplasmy
Evaluate mitochondrial genetic disorders by evaluating changes in _____.
mtDNA (not able to repair DNA and replicates independently of nDNA)
Heteroplasmy - mother may contribute two different populations - mutant and normal - and then during replication they will segregate randomly so that :
Some cells get more mutant mitochondria than others during development
-Replication of Mitochondria is controlled by amount of ATP (independent)
Phenotype is usually displayed in high energy tissues such as ______ and the ______. So that they will present with muscle _____ and ______ symptoms
Skeletal muscle
Brain
Weakness
Neurological
Quantify the amount of mutant mitochondria in a cell through ______ ______.
restriction mapping - can track heritable mutation
If a male presents with symptoms characteristic of an mtDNA disorder, what is the likelihood that his children will also present with the disease?
0%- mtDNA defects are only passed through the mother
Complex _____ aka ______ is not required for oxidative phosphorylation because it does not span the mitochondrial membrane. It accepts which coenzyme?
Complex II
FADH/succinate dehydrogenase
FAD(H2)
Complex 1 is aka?
NADH dehydrogenase
CoQ is aka?
Quinone derivative
Complex II is aka?
FADH/succinate dehydrogenase
Complex III is aka?
Cytochrome c and b
Complex IV is aka ?
Cytochrome c, a and a3
Complex V is aka?
ATP synthase
Uncouplers disrupt the mitochondrial membrane and reduce ATP product and ____ oxygen consumption.
Increase
NADH or FADH2 generated in the cytosol of cell must be ____ _____ into the mitochondria.
transported actively
Succinate is a substrate for which complex in the ETS?
Complex 2- coupled to TCA cycle and accepts succinate rather than malate as substrate
Mechanical work is best described as ?
conversion of a high energy bond to instigate a conformational change in a protein
In the case of an exothermic reaction, what would Delta G NOT be ?
Negative - indicative of a spontaneous reaction
What is Delta S described as ?
change in entropy or an increase in disorder and this value is often negligible in reactions
The last cytochrome in the ETC, cytochrome oxidase, passes electrons to O2. Cytochrome oxidase is able to do this because ….
it has lower Km for oxygen then hemoglobin
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 _____.
Cytochrome oxidase
oxygen
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.
exergonic
negative
What is Delta H ?
Change in enthalpy- measurement of total heat content
-equal to the internal energy of system
What is Delta S ?
Change in entropy , or increase in disorder
What is an example of biochemical work ?
Anabolic pathways - synthesis of DNA, glycogen, proteins)
What is an example of Transport work ?
(active transport)- ATP used to move compounds against gradient
-Na+/K+ pump ATPase
What is an example of Mechanical work ?
high energy bond is converted into movement by changing conformation of protein
- contracting muscle fibers
- motor proteins that transport chemicals along fibers
What does NADPH stand for ?
Nicotinamide adenine dinucleotide phosphate
What does FAD stand for ?
Flavin adenine dinucleotide
True or False:
NAD and NADP have the same reduction potential
True
The more ______ a reduction potential of a compound, the greater is the energy avaliable for ATP generation.
NADH has a more _____ potential than FAD.
negative
negative
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.
Ribose
ATP
What is the reducing agent?
The element or compound that loses or “donates” an electron to another compound
(the reducing agent is the one that gets oxidized)
What is the oxidizing agent?
The compound that gains or accepts electrons and hence oxidizes another compound
(the oxidizing agent is the one that gets reduced)
Can ADP, ATP, phosphate, pyruvate , and other metabolites move freely across the Inner mitochondria membrane ?
no- they must be transported through inner and outer membranes
What is able to make it through the outer membrane that is more permeable in the mitochondria ?
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
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
Ca+
In a temporary lack of Oxygen (O2), the ATP synthase will do what?
Run backwards and hydrolyze the ATP back into ADP +P to try to maintain equilibrium
What is DHAP , where is it found?
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
FAD in the mitochondria is contained in what (relative to Glycerol 3-phosphate shuttle)
FAD is contained in glycerol phosphate dehydrogenase
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
-3
The Delta G for a series of reactions is additive
The fully reduced quinol form of CoQ contains what combination of electrons and protons
2 electrons and 2 protons
