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Metabolism is the sum of...
All the chemical transformations that occur in living cells
Metabolic pathways are _____ and permit ___ of building blocks between the various pathways
Metabolism is essential for generation of what?
What does the term intermediary metabolism refer to?
Reactions that involve the interconversion of small molecules < or = 1000 Da (1 dalton = mass of 1 proton)
What are the 2 major processes of metabolism?
What is catabolism?
- The breakdown of energy-containing nutrients (convergent)
- Release energy (some is lost as heat)
What is anabolism?
- Use small compounds as building blocks (divergent)
- Use energy
Catabolism releases energy as...
- 1. ATP
- 2. Reduced electron carriers
- 3. Heat
Which 2 things are used as energy to power anabolic reactions?
Thermodynamics deals with...
- Systems proceeding toward equilibrium
- Systems are a mixture of reactants and products?
What is Gibbs free energy?
- Symbol - G
- Free energy in the system and is related to enthalpy, entropy, temperature
What is the equation for calculating G?
G = H - TS
What is the enthalpy?
- Symbol - H
- Heat content related to number and type of bonds
What is entropy?
- Symbol - S
- Extent of disorder in the system (this value is low for organized systems)
What is temperature measured in for the Gibbs free energy equation?
Kelvin (25°C = 298K)
What is ΔG? (Δ is delta)
The change in free energy conctent as the reaction progresses (constant temperature and pressure)
What is the equation for ΔG?
ΔG = ΔH - TΔS
What does it mean when ΔG is negative?
-xkJ/mol energy is released (exergonic/spontaneous)
What does it mean when ΔG is positive?
xkJ/mol energy is released (endergonic)
What does it mean when ΔG is zero?
The reaction is at equilibrium.
What is an important example of an exergonic reaction?
- The oxidation of glucose
- C6H12O6 + 6O2 --> 6CO2 + 6H2O
- ΔG = -2840kJ/mol
The oxidation of glucose occurs ___ in the cell, but glucose in the presence of oxygen is ___ and will not ____ because it needs..
- It needs energy of activation
ΔG is independent of... and provides...
- The reaction mechanism
- No information on the reaction rates (difference between energy of substrate and products)
To compare the amount of energy released during different reactions, reactions are compared...
Under standard conditions
What is ΔG0?
Standard free energy change (298K, 1atm, solutions at 1M)
What is ΔG'0?
Biochemical standard free energy change (298K, 1atm, solutios at 1M, pH 7.0)
How to calculate ΔG for a reaction?
A + B <-----> C + D
- ΔG = ΔG'0 + RTln( [C][D].................................[A][B])
- where R= gas constant (8.315J/mol K)
- T= temperature in K
At equilibrium, the rate of conversion of A&B to C&D is equal to what?
The rate of converison on C&D to A&B
How to calculate ΔG'0?
ΔG'0 = -RTlnK'eq
If the ΔG'0 for reactions are known, it is possible to determine the...
Total energy changes for coupled reactions
ATP is used as the primary ebergy source used to power what?
What are high energy compounds?
Compounds that have a ΔG'0 of hydrolysis thats > -25kJ/mol
What is the chemical basis for the energy stored in the phosphoanhydride bonds? (4 things)
- 1. At pH 7 ATP carries four negative charges (hydrolysis releases electrostatic stress)
- 2. Resonance delocalization of PO42-3. ADP ionizes releasing a proton (ie increases ΔS)
- 4. ATP hydrolysis increase the solvation of ADP and Pi
What is primary energy storage molecule in the cell?
What are some examples of where energy can be stored in the form of reducing electron carriers?
NADH, NADPH, FADH2
How are electrons transported in biological systems?
As a hydride (a proton with 2 electrons (H-))
How can you monitor the flow of electrons?
By using a voltmeter
What does the equilibirum point for a redox reaction depend on?
The relative affinity of Aox and Box for electrons
What is E0?
The reduction potential tendency to gain electrons
What is E'0?
The reduction potential at (1M, 1atm, 25°C, and pH 7.0)
The more negative the E'0, the more...
Reducing potential and the lower the affinity for electrons will readily donate
How can we describe the relationship between ΔE'0 and ΔG'0?
- ΔG'0= -nFΔE'0where n=number of electrons transferred
- F=Faraday constant (96.5 kJ/Vmol)
What does a negative E'0 mean?
It is an electron donor
What does a positive E'0 mean?
It is an electron acceptor
What is the alternate name for glycolysis?
The Embden-Meyerhoff-Parnas Pathway
What is one of the oldest biochemical paths that is conserved in almost all living cells?
What does glycolysis exploit?
The fact that the major energy source for most organisms is glucose
Glycolysis provides a stepwise degradation of the hexose glucose into what?
#3 carbon unit pyruvate, ATP, and NADH (ΔG'0= -2840kJ/mol)
Is glycolysis aerobic or anaerobic?
Anaerobic (but only 5% energy capture without oxidative phosphorylation)
Where does glycolysis occur for most organisms?
In the cytosol
Where does glycolysis occur for kinetoplstid protozoan parasites?
In the glycosome
What are the 2 phases of glycolysis? Describe them
- 1. Prepatory phase, cost energy (ie, uses ATP)
- 2. Payoff phase, produces ATP and NADH
What is the overall chemical reaction for glycolysis?
Glucose + 2 ADP + 2 NAD+ + 2 Pi ---> 2 pyruvate + 2 ATP + 2 NADH + 2 H2O
Glycolysis requires what to start to drive the catabolism?
Describe the 1st priming reaction (1st step of glycolysis)?
- Phosphorylation of glucose at carbon 6
- 1 ATP used (reaction is unfavorable)
- Catalyzed by hexokinase (hexokinase use ATP to generate G-6-P)
- High levels of G-6-P inhibit hexokinase
- Glucose is activated
- Product is glucose 6-phosphate
- ΔG'0 = 13.8kJ/mol (not spontaneous)
2nd step of glycolysis:
What happens to the glucose 6-phosphate?
- Becomes fructose 6-phosphate (isomerization)
- Catalyzed by phosphohexose isomerase or glucosephosphate isomerase
- The C-2 hydroxyl is oxidized to a ketone via an enediol intermediate
- Not thermodynamically favorable but is pushed forward by coupling to other reactions in the glycolytic pathway
- ΔG'0 = 1.7kJ/mol
Describe the 2nd priming reaction (3rd step of glycolysis)?
- Fructose 6-phosphate becomes fructose 1,6-biphosphate
- 1 ATP used (reaction is not favorable)
- Catalyzed by phosphofructokinase-1
- Transfers phosphoryl group from ATP
- PFK-1 is a major point for the regulation of glycolysis (ATP and citrate from TCA cycle are inhibitors of PFK-1, while ADP, AMP, and F-2,6-P are activators (ie when ATP, the main goal of glycolysis is high, there is no need to make more, so this is a good place to stop the production)
- ΔG'0 = -14.2kJ/mol
4th step of glycolysis:
What happens to the fructose 1,6-biphosphate?
- Cleavage of 6-carbon sugar phosphate to 2 3-carbon sugar phosphates
- Catalyzed by aldolase
- Thermodynamically unfavorable, driven by rapid removal of G-3-P
- Yields 2 different triosephosphates (glyceraldehyde 3-phosphate (G-3-P, aldose) and dihydroxyacetone phosphate (DHAP, ketose))
- ΔG'0 = 23.8kJ/mol
5th step of glycolysis:
What happens to the 2 triosephosphates?
- Only the glyceraldehyde 3-phosphate can be directly degraded, so the dihydroxyacetone phosphate is rapidly and reversibly converted to glyceraldehyde 3-phosphate which is catalyzed by triosephosphate isomerase (TIM).
- Driven by coupling this process to other glycolytic reactions which have a large negative ΔG'0.
- Readily reversible
- ΔG'0 = 7.5kJ/mol
6th step of glycolysis:
What happens to the glyceraldehyde 3-phosphate?
- Glyceraldehyde 3-phosphate is oxidized and phosphorylated
- Catalyzed glyceraldehyde-3-phosphate dehydrogenase
- This is the first energy conserving reaction (2 NADH/glucose produced)
- Product is 1,3-Bisphosphoglycerate
- ΔG'0 = 6.3kJ/mol
- ΔG = -1.3kJ/mol at 37°C using steady state concentration in red blood cell
- Aldehyde group of G-3-P reacts with an active site sulfhydryl group (cysteine) on enzyme
- Formation of covalent intermediate resulting in the transfer of a hydride group to NAD+ to form NADH
- NADH is released from the enzyme and Pi attach the thiol acyl bond releasing G-1,3-P
Describe the first ATP-forming reaction (7th step of glycolysis)?
- Substrate-level phosphorylation
- 2 ATP produced
- Catalyzed by phosphoglycerate kinase
- Phosphoglycerate kinase transfers high-energy phosphoryl group from carboxyl group of 1,3-bisphosphoglycerate to ADP, forming ATP and the product 3-phosphoglycerate
- ΔG = -18.5kJ/mol
8th step of glycolysis:
What happens to the 3-phosphoglycerate?
- Catalyzed by phosphoglycerate mutase
- Reversible shift of the phosphoryl group between carbon 3 and carbon 2
- Occurs via 2 steps with the formation of the intermediate 2,3-bisphosphoglycerate
- Magnesium is essential (Mg2+)
- Product is 2-phosphoglycerate
- ΔG'0 = 4.4kJ/mol
9th step of glycolysis:
What happens to the 2-phosphoglycerate?
- Catalyzed by enolase, which promotes reversable removal of H2O from 2-phosphoglycerate, dehydration of 2-PG to form a high energy phosphate bond
- Involves an enolytic intermediate stabalized by Mg2+
- Product is phosphoenolpyruvate (PEP)
- ΔG'0 = 1.8kJ/mol
What is the 2nd ATP-forming reaction (10th and last step of glycolysis)?
- Substrate-level phosphorylation
- Transfer of phosphoryl to ADP to make 2 ATP/glucose
- Catalyzed by pyruvate kinase
- Requires potassium (K+) and either Mg2+ or manganese (Mn2+)
- Product is pyruvate
- ΔG = -31.4kJ/mol
How much glucose in the blood?
How is glucose taken into the cell and where does it go?
- By transporters
- Trapped in cytosol by phosphorylation
What are the 4 regulatory steps of glycolysis?
- 1. Hexokinase in step 1 is inhibited by ATP and G-6-P
- 2. Phosphofructokinase in step 3 is inhibited by citrate and ATP, activated by F-2,6-P and AMP
- 3. Glyceraldehyde-3-phosphate dehydrogenase in 6th step is regulated by the levels of NAD+4. Pyruvate kinase in step 9 is inhibited by acetyl-coA and ATP, activated by F-1,6-P and AMP
How much energy do the 2 pyruvates from glycolysis retain in glucose?
What is the process of generating NAD+ from NADH termed?
What is TCA?
The tricarboxylic acid cycle
How is the 90% of energy remaining in the 2 pyruvate molecules harvested?
In the TCA cycle and oxidative phosphorylation
Where do the TCA cycle and oxidative phsophorylation take place?
In the mitochondria of eukaryotic cells
What are the parts of a mitochondria?
An outer membrane, then an inter-membrane space, and inner membrane, then the inner mitochondria space (matrix)
What are cristae?
The extensive inward folds of the inner membrane of a mitochondria
The energy released during TCA and oxidative phosphorylatin is captured as what?
Where is ATP produced?
In the mitochondrial matrix
Where and how is ATP transported after it is produced?
It is exported to the cytosolic space by exchangers (membrane transporters)
What are porins?
Large permeable channels in the outer mitochondrial membrane that allow compounds smaller than 5,000 Da to pass freely
Describe the inner mitochondrial membrane:
(please! :] )
- Highly impermeable
- Contains transport proteins (carriers) that transport specific substrates
- -succinate dehydrogenase complex
- -NADH dehydrogenase complex
- -electron transport chain components
What does the mitochondrial matrix contain?
- Soluble enzymes of TCA cycle
- Pyruvate dehydrogenase complex
- DNA & ribosomes
What does the intermembrane space contain?
Enzymes (like adenylate kinase: ATP + AMP --> 2ADP)
What is TCA also known as?
The citric acid cycle or Krebs cycle
What is the overall TCA reaction?
Acetyl-CoA + 3NAD+ + FAD + GDP + Pi + 2H2O ---> 2CO2 + 3NADH + FADH2 + Co-ASH + GTP + 2H+
What is the prelude step to the Krebs cycle?
- Pyruvate, which is made in the cytosol, enters the mitochondria and is decarboxylated and coupled to Coenzyme A (Co-A) and produces one NADH molecule
- This is catalyzed by pyruvate dehydrogenase complex
- ΔG'0 = -33.4kJ/mol
How is the TCA cycle regulated?
- 3 ways:
- 1. Citrate synthase (inhibited by succinyl-CoA, citrate, ATP, and NADH, where ATP and NADH levels determine energy status of the cell)
- -In resting cells: NADH/NAD+ and ATP/ADP ratios are high
2. Isocitrate dehydrogenase (inhibited by high levels of ATP and NADH, activated by high levels of ADP and NAD+
3. α ketoglutarate dehydrogenase (inhibited by high levels of NADH and succinyl-CoA, activated by high levels of AMP)
What is ETC?
The Electron Transport Chain
Is aerobic or anaerobic respiration more efficient?
Oxidation of glucose or fatty acids provides much more energy than what?
Oxygen serves as the terminal acceptor for what?
Electrons carried by NADH and FADH2
Oxygen is reactive and makes what?
Toxic intermediates (cell evolved detoxification enzymes like catalase, superoxide dismutase)
What are 3 properties of oxygen that favor energy extraction?
- It is abundant (~21% of air)
- It diffuses through membranes
- It is very reactive and easily accepts electrons
Where is ETC organized as a chain?
On the inner mitochondrial membrane
What is a quick summary of ETC?
High energy electrons extracted for carbon sources (glucose, fatty acid) on NADH and FADH2 are transported to oxygen via the transportation down an electron chain. Chemical energy is generated in the process.
What does electron transfer down the ETC decrease?
The reduction potential (ΔE'0)
What is the ΔE'0 for transfer of electrons from NADH to oxygen?
ETC consists of how many complexes located on the inner mitochondrial membrane?
What is Complex I for ETC?
What is Complex II for ETC?
What is Complex III for ETC?
Cytochrome b1 complex
What is Complex IV for ETC?
What are key components used to carry electrons through the ETC chain?
quinones, iron-sulfur proteins, cytochromes
What are quinones?
- Hydride carriers
- Anchored to inner mitochondrial membrane (via the isoprenoid tail which (n~10))
- Mobile inside the membrane
- Thought to sit on the hydrophobic core
Quinones accept electrons from what?
NADH and FADH2
How do quinones carry electrons?
- The 2-step reduction allows quinones to carry electrons one of 2 ways:
- -Either 2 electrons as dihydroquinone
- -Or 1 electron as semiquinone
What are iron-sulfur proteins?
- Also called iron-sulfur centers (FeS)
- Contain 2, 3, 4, or 8 iron atoms bound to a protein via chelation with cysteine residues
- Sulfur also forms a bride between irons
- 4-Fe centers have a tetrahedral structure resembling a cube
Iron-sulfur centers transfer how many electrons at one time?
How do iron-sulfur clusters transfer electrons?
Transfer is coupled to the red-ox reaction (Iron-sulfur clusters under red-ox without binding protons)
What is the equation for the red-ox reaction associated with iron-sulfur centers?
2Fe3+ + 1e- <---> Fe3+ + Fe2+
How do cytochromes transfer electrons?
- Involves a heme group (a prosthetic group that contains iron that it chelated by 4 nitrogen groups)
- The heme groups in the 3 cytochromes (a, b, & c) differ by the types of substituents attached to the porphyrin ring
- Cytochromes transfer 1 electron using the single iron center
Which of the 3 cytochrome's heme group is covalently attached to the protein backbone via cysteine residues?
What is the equation associated with the transfer of electrons in cytochromes?
Fe3+ + 1e- <---> Fe2+
What is Complex I in ETC?
What is the mitochondrial location of Complex I (NADH Dehydrogenase)?
How many subunits does Complex I (NADH Dehydrogenase) have?
What are the prosthetic groups of Complex I (NADH Dehydrogenase)?
- 7 Fe-S clusters
- Coenzyme Q
What is Complex II in ETC?
What is the mitochondrial location of Complex II (Succinate Dehydrogenase)?
How many subunits does Complex II (Succinate Dehydrogenase) have?
What are the prosthetic groups of Complex II (Succinate Dehydrogenase)?
What is Complex III in ETC?
Cytochrome b1 Complex
What is the mitochondrial location of Complex III (Cytochrome b1 Complex)?
How many subunits does Complex III (Cytochrome b1 Complex) have?
What are the prosthetic groups of Complex III (Cytochrome b1 Complex)?
- Cyt b sub H
- Cyt b sub L
- Cyt c sub 1
- 1 Fe-S cluster
What is Complex IV in ETC?
What is the mitochondrial location of Complex IV (Cytochrome oxidase)?
How many subunits does Complex IV (Cytochrome oxidase) have?
What are the prosthetic groups of Complex IV (Cytochrome oxidase)?
- CuA/CuBFe-Cu center
- Heme A sub 3
What does energy recovery from electrons carried by NADH depend on?
Complexes I, III, & IV
How do electrons pass from one complex to another?
Using the Q cycle and soluble cytochrome c proteins
Describe the movement of electrons in Electron Transport Complex I
- 1. Electrons from NADH go to FMN forming FMNH2
- 2. Those go to 2 Fe-S clusters, one electron at a time
- 3. Those go to UQ (coenzyme Q)
The electron movement from NADH to UQ causes movement of H+
into the intermembrane space (Unknown mechanism)
What is the equation for the movement of electrons in Electron Transport Complex I?
NADH + Q + 5H+matrix ---> NAD+ + QH2 + 4H+intermembrane
Describe the mechanism of Electron Transport Complex III
- CoQH2-cytochrome c oxidoreductase catalyzes the oxidation of UQH2 by passing electrons to cytochrome c (in matrix)
- The conversion of ubiquinone to dihydroguinone requires reduction of Fe3+ to Fe2+ requires only 1 electron
- 2 molecules of cyt c required for each UQH2
- Protons pumped out into the intermembrane space
Why are protons pumped out into the intermembrane space in Electron Transport Complex III?
Cytochromes carry electrons but not protons, so they are pumped out
What is the equation for Electron Transport Complex III?
QH2 + 2Cyt c ox + 4H+matrix ---> 2Cyt cred + Q + 4H+intermembrane
What does cytochrome c oxidase catalyze in Electron Transport Complex IV?
The transfer of electrons from cytochrome c to oxygen
Are protons pumped out into the intermembrane space in ETC IV?
Are protons pumped out into the intermembrane space in ETC I?
How do the electrons flow in ETC IV?
From cyt c to CuA/CuB, then to cytochrome a, then to cytochrome a3-CuB, then to O2
How many H+ and e- are shuttled through complex IV?
4H+ and 4e-
How are electrons from the coenzyme FADH2 fed into the elctron transport chain?
Through Complex II which also uses the Q cycle
How does Complex II move electrons?
Consists primarily of the TCA enzyme succinate dehydrogenase + 2Fe-S proteins to move electrons
Where is the enzyme inserted in Complex II?
Into the inner mitochondrial membrane leaflet facing the matrix
When does Complex II capture electrons?
Captures the FADH2 electrons generated by oxidation of succinate to fumarate
Where are the electrons passed to after being captured in Complex II?
Electrons are passed to conenzyme Q (UQ) which transfers electrons to Complex III
What is the ΔG'0 of the Electron Transport Complex?
How many molecules of ATP does NADH oxidation produce?
2.5 molecules of ATP for every electron pair transferred to oxygen
How many molecules of ATP does FADH2 oxidation produce?
1.5 molecules of ATP for every electron pair transferred to oxygen
What inhibits Complex I?
- Blocked by rotenone amyta
- (broad spectrum pesticide found in roots of several different plants)
What inhibits Complex III?
- Blocked by antimycin A
- (fungicide produced by Streptomyces)
What inhibits Complex IV?
Blocked by CN-, N-3, CO
What is Chemiosmotic theory also known as?
Who proposed the chemiosmotic coupling theory?
- Peter Mitchell in the 1960s
- (won the Nobel Prize in 1978)
What is the idea behind the chemiosmotic hypothesis?
Energy is released by the movement of electrons down the ETC, this energy is used to drive the synthesis of ATP via the chemiosmotic hypothesis
What are the 3 principles behind chemiosmotic theory?
- 1. ETCs are organized in the inner mitochondrial membrane, electrons move down the chain and finally donate to oxygen, proteins extrude into the intermembrane space
- 2. Movement of electrons generates an electrical potential (ψ psi) and a proton gradient (ΔpH) across the inner membrane. This electrochemical gradient is also known as the proton motive force.
- 3. The flow of electrons through the ATP synthase into the mitochondrial matrix drives the synthesis of ATP
What is the proton motive force?
- The electrochemical gradient made up of the movement of electrons generating an electrical potential and a proton gradient across the inner membrane
- Δp - the sum of the electrical and chemical components of the transmembrane proton gradient
ΔpH = ?
pHout - pHin (proton gradient)
Δψ = ?
ψout - ψin (electical gradient)
A proton motive force across the inner mitochondrial membrane is described by which equation?
- Δp = Δψ - zΔpH
- (where z = conversion factor 61.8mV at 37°C)
What are the 3 major pieces of evidence supporting chemiosmotic theory?
- 1. Substrate oxidation by respiring mitochondria or bacteria (in the presence of O2) expel protons and drop pH in the intermembrane space (ΔpH ~ 0.05 units)
- 2. ATP synthesis is halted by disruption of inner membrane integrity
- 3. Uncouplers (small molecules like dinitrophenol or gramacidin) that dissipate proton gradient, stop ATP synthesis
What are uncouplers?
Small molecules that inhibit the coupling between the electron transport and phosphorylation reactions (like dinitrophenol or gramacidin)
ATP synthase is compoosed of which 2 major components?
- 1. F1-ATP synthesis activity (5 subunits 3α, 3β, γ, δ, ε) has 3 nucleotide binding sites
- 2. F0- Transmembrane channel for protons (3 subunits a, 2b, 12c)
What causes the rotation of the rotating portion of ATP synthase?
Driven by the proton motive force (Δp)
Describe the structure of ATP synthase
- Revolving "c" ring is attached to shaft (made up of γ, ε) which rotates within the stationary α, β hexamer
- Rotation is counterclockwise for ATP synthesis and clockwise if ATP is hydrolyzed.
What does sythesis of 1 ATP by synthase require?
3H+, and 1H+ needed to drive the ATP/ADP exchange out of the matrix