unit 2 week 2 pt 3 Flashcards
Why are mitochondria often compared to power plants?
Like power plants, mitochondria extract energy from organic materials and store it as electrical energy. This energy is used to create an ionic gradient across the inner mitochondrial membrane, which can then be used to perform cellular work.
How do ionic gradients function as a source of energy in cells?
An ionic gradient across a membrane is a form of stored energy that can be used for various functions: intestinal cells use it to transport sugars and amino acids; nerve cells use it to conduct neural impulses; mitochondria use it to synthesize ATP. Three key components are required: a system to generate the gradient, a membrane capable of maintaining the gradient, and machinery to use the gradient for work (e.g., ATP synthesis).
What is oxidative phosphorylation, and how does it differ from substrate-level phosphorylation?
Oxidative phosphorylation synthesizes ATP using energy released from electrons during substrate oxidation in the mitochondria, making it the primary way cells produce ATP. In contrast, substrate-level phosphorylation forms ATP by the direct transfer of a phosphate group from a substrate molecule to ADP, occurring during glycolysis and the TCA cycle but producing significantly less ATP.
-diff explanation:
Oxidative phosphorylation (OP) generates ATP by using the energy from electron transport, while substrate-level phosphorylation (SLP) directly transfers a phosphate group from a substrate to ADP to form ATP. SLP is a direct transfer of a phosphate group from a high-energy substrate (like phosphoenolpyruvate or succinyl-CoA) to ADP, forming ATP.
How significant is oxidative phosphorylation in ATP production?
It produces an estimated 2 × 10^26 molecules of ATP per day, which is over 60 kg of ATP in a human body, making oxidative phosphorylation the dominant ATP-generating process in most cells.
Why is understanding oxidative phosphorylation important?
Discovering the mechanism of oxidative phosphorylation has been a major milestone in cell and molecular biology. Ongoing research continues to explore unanswered questions about how substrate oxidation releases free energy to power ATP synthesis.
How are oxidizing agents ranked?
Oxidizing agents are ranked based on their affinity for electrons—the greater the affinity, the stronger the oxidizing agent.
-details:
-Oxidizing agents are ranked by their standard reduction potentials, with those having higher positive values being stronger oxidizing agents, meaning they have a greater tendency to gain electrons and be reduced.
-Standard Reduction Potential:
This value indicates the tendency of a substance to be reduced (gain electrons) under standard conditions.
Strong Oxidizing Agents:
Substances with high (positive) standard reduction potentials are strong oxidizing agents because they readily accept electrons and are easily reduced.
Weak Oxidizing Agents:
Substances with low (negative) standard reduction potentials are weak oxidizing agents because they have a lower tendency to gain electrons and are less easily reduced.
How are reducing agents ranked?
Reducing agents are ranked based on their electron transfer potential—the lower the affinity for electrons (i.e., the more easily electrons are released), the stronger the reducing agent.
-details:
-Reducing agents are ranked by their standard reduction potentials, with stronger reducing agents having more negative potentials, indicating a greater tendency to lose electrons and be oxidized.
What is an example of a strong reducing agent?
NADH is a strong reducing agent because it has a high electron transfer potential.
What is an example of a weak reducing agent?
H2O is a weak reducing agent because it has a low electron transfer potential.
How do oxidizing and reducing agents relate in a couple?
Strong reducing agents are paired with weak oxidizing agents, and vice versa.
Give an example of an oxidation-reduction couple.
The NAD+/NADH couple, where NAD+ is a weak oxidizing agent, and NADH is a strong reducing agent.
What is an oxidation-reduction potential (redox potential)?
It is the measure of a substance’s affinity for electrons, detected as voltage relative to a standard couple.
What is the standard couple used for redox potential measurements?
The hydrogen couple (H+/H2) is the standard, with an assigned redox potential of 0.00 V under standard conditions.
What are the standard conditions for measuring redox potential?
1.0 M solute concentrations, 1 atm pressure for gases, and a temperature of 25°C.
Why is the redox potential of hydrogen listed as -0.42 V instead of 0.00 V in biological systems?
This value is measured at pH 7.0 (10^-7 M H+), which is more physiologically relevant than the standard pH 0.0 condition.
How are redox potential values assigned?
Couples with strong reducing agents (good electron donors) have more negative redox potentials. Couples with strong oxidizing agents (good electron acceptors) have more positive redox potentials.
What is the standard redox potential (E°’) for the NAD+/NADH couple?
-0.32 V.
How does acetaldehyde compare to NADH as a reducing agent?
Acetaldehyde is a stronger reducing agent than NADH, with a more negative redox potential (-0.58 V).
How is the standard free-energy change (ΔG) related to redox potential?
ΔG = -nFΔE°, where n = number of electrons transferred, F = Faraday constant (23.063 kcal/V·mol), and ΔE° = difference in standard redox potential between two couples.
-more: they’re inverse!
If E° is positive, then ΔG° is negative, indicating a spontaneous reaction.
If E° is negative, then ΔG° is positive, indicating a non-spontaneous reaction.
What is the ΔG for the oxidation of NADH by O2?
-52.6 kcal/mol.
How does this free-energy change relate to ATP synthesis?
The energy released from NADH oxidation (-52.6 kcal/mol) is sufficient to drive ATP formation (ΔG = 7.3 kcal/mol) under cellular conditions.
How is this energy transfer carried out in the mitochondrion?
Through a series of small, energy-releasing steps to optimize ATP synthesis.
Which TCA cycle intermediates transfer electrons to NAD+?
Isocitrate, α-ketoglutarate, and malate, as they have highly negative redox potentials.
Why does succinate oxidation require FAD instead of NAD+?
The succinate/fumarate couple has a more positive redox potential, requiring FAD, which has a greater electron affinity than NAD+.
What role do dehydrogenases play in electron transport?
Dehydrogenases transfer pairs of electrons from substrates to coenzymes. Five out of nine reactions in the TCA cycle are catalyzed by dehydrogenases, generating NADH and FADH2.
Where do NADH molecules go after being formed in the mitochondrial matrix?
NADH molecules dissociate from their respective dehydrogenases and bind to NADH dehydrogenase (Complex I), an integral protein in the inner mitochondrial membrane.
What is unique about succinate dehydrogenase?
Succinate dehydrogenase (catalyzing the formation of FADH2) is the only enzyme of the TCA cycle embedded in the inner mitochondrial membrane and is also a part of Complex II in the electron transport chain.
How are electrons transferred from NADH and FADH2?
Electrons from NADH and FADH2 enter the electron transport chain (ETC), which consists of specific electron carriers embedded in the inner mitochondrial membrane, ultimately reducing O2 to H2O and generating a proton gradient for ATP synthesis.
What are the five types of membrane-bound electron carriers in the electron transport chain (ETC)?
Flavoproteins (contain FAD or FMN), cytochromes (contain heme prosthetic groups), copper atoms (found in a single protein complex), ubiquinone (Coenzyme Q, UQ) (a lipid-soluble molecule), and iron-sulfur proteins (contain iron linked to sulfide ions).
What are flavoproteins, and what is their function?
Flavoproteins consist of a polypeptide bound to FAD or FMN, both derived from riboflavin. They accept and donate 2 protons (H+) and 2 electrons (e-). Major flavoproteins include NADH dehydrogenase (Complex I of ETC) and succinate dehydrogenase (Complex II of ETC, also part of the TCA cycle).
How do cytochromes participate in electron transport?
Cytochromes are proteins containing heme prosthetic groups. The iron atom in the heme undergoes reversible oxidation between Fe3+ (oxidized) and Fe2+ (reduced) as it accepts or donates a single electron.
What role do copper atoms play in the ETC?
Three copper atoms are found in a single protein complex in the inner mitochondrial membrane. They accept and donate single electrons, cycling between Cu2+ (oxidized) and Cu+ (reduced) states.
What is ubiquinone (Coenzyme Q), and why is it important?
Ubiquinone (UQ or CoQ) is a lipid-soluble electron carrier with a long hydrophobic chain. It can accept and donate 2 electrons and 2 protons, existing in three states: fully oxidized (UQ), partially reduced radical form (UQ•-), and fully reduced (UQH2). It remains in the lipid bilayer and diffuses rapidly between electron transport complexes.
What are iron-sulfur proteins, and how do they function in electron transport?
Iron-sulfur proteins contain iron atoms bound to sulfide ions, rather than heme. Common types of iron-sulfur centers include [2Fe-2S] clusters and [4Fe-4S] clusters, transferring a single electron despite containing multiple iron atoms.
How is the sequence of electron carriers in the ETC determined?
Scientists used inhibitors (e.g., rotenone, antimycin A) to block electron transport at specific sites and measured oxidation states of carriers. Spectrophotometry was used to detect whether carriers were in their oxidized or reduced states.
How do electrons travel between electron carriers?
Electron transfer depends on the redox potential difference between carriers. Electrons move ‘downhill’, losing energy at each step, ultimately reducing O2 to H2O, through special ‘tunneling pathways’ composed of covalent and hydrogen bonds.
What are the four electron-transport complexes in the inner mitochondrial membrane?
The four electron-transport complexes are Complexes I, II, III, and IV, each with a distinct role in the oxidation pathway.
What are the two electron carriers that are not part of these complexes?
Ubiquinone (coenzyme Q) and cytochrome c are mobile electron carriers that shuttle electrons between the complexes.
Where are ubiquinone and cytochrome c located?
Ubiquinone is dissolved in the lipid bilayer, while cytochrome c is a soluble protein in the intermembrane space.
What is the function of ubiquinone and cytochrome c?
They transport electrons between the large, relatively immobile electron-transport complexes within the mitochondrial membrane.
How do electrons enter the respiratory chain?
Electrons from NADH enter through Complex I, which transfers them to ubiquinone, forming ubiquinol. Electrons from FADH2 enter through Complex II, which transfers them directly to ubiquinone, bypassing Complex I.
Why does FADH2 bypass Complex I?
Complex I has a too negative redox potential to accept electrons from FADH2, so they are transferred directly to ubiquinone via Complex II.
Which three complexes function as proton pumps?
Complexes I, III, and IV act as proton pumps, transferring protons across the inner mitochondrial membrane.
What happens when electrons move through these complexes?
At three key sites, electron transfer releases free energy, which is used to pump protons from the mitochondrial matrix to the intermembrane space, creating a proton gradient.
What is a proton conduction pathway (proton wire)?
It is a network of acidic residues, hydrogen-bonded residues, and trapped water molecules that allow H+ ions to ‘hop’ through a channel, facilitating proton movement.
How does the proton gradient contribute to ATP synthesis?
The proton gradient created by Complexes I, III, and IV drives ATP synthesis by allowing protons to flow back through ATP synthase, generating ATP.
How can the proton-pumping function of these complexes be demonstrated?
Each complex can be purified and incorporated into artificial lipid vesicles, where they can still accept electrons and pump protons across the vesicle membrane.
How do bacterial electron-transport complexes differ from mammalian ones?
Bacterial complexes have fewer subunits. The additional subunits in mammalian complexes do not participate in electron transport but are thought to assist in regulation or assembly.
How has the electron-transport process evolved?
Despite structural differences, the fundamental electron-transport mechanism has remained largely unchanged since its evolution in prokaryotic ancestors billions of years ago.
What is the function of Complex I in the electron-transport chain?
Complex I catalyzes the transfer of electrons from NADH to ubiquinone (UQ), forming ubiquinol (UQH2), marking the gateway to the electron-transport chain.
What is the structure of Complex I?
Complex I consists of two portions: a hydrophilic domain that projects into the matrix and a hydrophobic portion embedded in the membrane.
What are the two main activities required for the electron-transport chain that Complex I carries out?
Complex I carries out electron transfer and proton translocation.
Where do the components required for electron transfer reside in Complex I?
All the components required for electron transfer are located within the hydrophilic portion of Complex I.
How does electron transfer occur in Complex I?
FMN-containing flavoprotein oxidizes NADH at the complex’s tip. Electrons are transferred through seven iron-sulfur centers to a protein-bound ubiquinone near the membrane boundary.
What happens during the electron transfer from NADH to ubiquinone?
The transfer of a pair of electrons from NADH to ubiquinone is thought to be accompanied by the movement of four protons from the matrix into the intermembrane space.
How does Complex I translocate protons across the membrane?
The membrane-embedded domain of Complex I contains a long α-helix (HL), which is in contact with three discontinuous transmembrane helices. These helices form half channels that, when connected by polar amino acid side chains, create a pathway for proton translocation.
What happens when electrons move to ubiquinone in Complex I?
The movement of electrons to ubiquinone causes a conformational change in the complex, which induces lateral movement of helix HL, leading to the tilting of transmembrane helices. This change alters the ionic environment of proton-transferring residues, promoting proton movement across the membrane.
How is the mechanism of Complex I compared to a steam engine?
The mechanism of Complex I is compared to a steam engine, with helix HL acting as the piston that drives the movement of downstream elements in the proton translocation machinery.
What causes a conformational change in Complex I?
The movement of electrons to ubiquinone causes a conformational change in the complex, which induces lateral movement of helix HL, leading to the tilting of transmembrane helices.
What is the significance of Complex I dysfunction?
Dysfunction of Complex I has been linked to certain neurodegenerative disorders.
What is the structure of Complex II?
Complex II consists of four polypeptides: two hydrophobic subunits that anchor the protein in the membrane and two hydrophilic subunits that comprise the TCA cycle enzyme, succinate dehydrogenase.
What is the function of Complex II?
Complex II provides a pathway for feeding lower energy electrons from succinate to FAD to ubiquinone.
How do electrons travel through Complex II?
Electrons from FADH2 at the enzyme catalytic site travel a 40 Å distance through three iron-sulfur clusters to ubiquinone.
Does Complex II translocate protons?
No, electron transfer through Complex II is not accompanied by proton translocation.
What is the role of the heme group in Complex II?
The heme group helps to attract escaped electrons, preventing the formation of harmful superoxide radicals.
What is the function of Complex III?
Complex III catalyzes the transfer of electrons from ubiquinol to cytochrome c.
How many protons are translocated by Complex III?
Four protons are translocated across the membrane for every pair of electrons transferred through Complex III.
How does Complex III translocate protons?
Two protons are derived from ubiquinol entering the complex and two additional protons are removed from the matrix and translocated by a second molecule of ubiquinol.
What are the components of Complex III?
Complex III contains three subunits with redox groups: cytochrome b with two heme b molecules, cytochrome c1, and iron-sulfur protein.
What is unique about cytochrome b in Complex III?
Cytochrome b is the only subunit of Complex III encoded by a mitochondrial gene.
What is the final step of electron transport?
The final step involves the transfer of electrons from reduced cytochrome c to oxygen, forming water.
How many protons are translocated by Complex IV?
For every molecule of O2 reduced to H2O, eight protons are involved: four protons are consumed in the formation of two molecules of water and four protons are translocated across the membrane to the intermembrane space.
How does Complex IV function as a redox-driven proton pump?
Cytochrome oxidase catalyzes the reduction of oxygen and simultaneously expels protons from the matrix, which is measured as a drop in surrounding pH.
What is the role of cytochrome oxidase in proton movement?
Cytochrome oxidase drives proton movement through conformational changes caused by the energy released during electron transfer, leading to proton pumping across the inner mitochondrial membrane.
How is oxygen reduced to water in Complex IV?
Electrons are transferred from cytochrome c to a bimetallic copper center (CuA), then to a heme (heme a3), which together catalyze the reduction of O2 to H2O.
What is the challenge of reducing oxygen to water?
The process of reducing O2 to H2O requires four electrons and must occur efficiently to prevent the accidental release of partially reduced oxygen species, which could damage cellular macromolecules.
What happens to protons during the reduction of oxygen?
Four protons are consumed in the formation of water and four protons are pumped across the membrane, contributing to the electrochemical gradient.
How does the cytochrome oxidase structure contribute to proton translocation?
Researchers have identified potential proton conduits within cytochrome oxidase, but their precise role remains under investigation.
