unit 2 week 2 pt 4

Question 1

What generates the proton electrochemical gradient in the mitochondria?

Answer 1

The transport of electrons across the inner mitochondrial membrane creates the gradient.

Question 2

What did Humberto Fernandez-Moran discover in the 1960s?

Answer 2

He found spherical structures attached to the inner mitochondrial membrane, later identified as part of ATP synthase.
-details:
-ATP synthase is a molecular motor enzyme that synthesizes ATP, the cell’s primary energy currency, by using the energy of a proton gradient across a membrane. It’s found in mitochondria, chloroplasts, and bacterial membranes, playing a crucial role in energy production.
-ATP synthase’s primary function is to catalyze the synthesis of ATP from adenosine diphosphate (ADP) and inorganic phosphate (Pi).
Proton Gradient:
It uses the energy stored in the form of a proton gradient (a difference in proton concentration) across a membrane to drive this process.
Rotary Motor:
ATP synthase is a rotary motor, meaning it has a rotating part that is powered by the flow of protons.

Question 3

What is the function of the F1 sphere in ATP formation?

Answer 3

It serves as the catalytic site where ATP is synthesized from ADP and Pi.

Question 4

Why does the F1 sphere also act as an ATPase?

Answer 4

Enzymes catalyze both forward and reverse reactions, so under different conditions, it can hydrolyze ATP instead of synthesizing it.

Question 5

How does the Na+/K+ ATPase illustrate the reversibility of enzyme-catalyzed reactions?

Answer 5

Under experimental conditions, it can synthesize ATP instead of hydrolyzing it when ion gradients are reversed.

Question 6

What force drives ATP synthesis in mitochondria?

Answer 6

The proton-motive force, created by the electron transport chain, drives ATP formation.

Question 7

What are the two main components of ATP synthase?

Answer 7

The F1 head, which catalyzes ATP synthesis, and the Fo base, which is embedded in the inner membrane.

Question 8

What connects the F1 and Fo portions of ATP synthase?

Answer 8

A central stalk and a peripheral stalk.

Question 9

Where is ATP synthase found besides mitochondria?

Answer 9

In the plasma membrane of bacteria and the thylakoid membrane of chloroplasts.

Question 10

Why is ATP synthase sometimes called F1Fo ATPase?

Answer 10

In bacteria, it can work in reverse, using ATP to pump protons, but in mitochondria, it only synthesizes ATP.

Question 11

How many catalytic sites for ATP synthesis does each F1 unit have?

Answer 11

Three, located on the ? subunits.

Question 12

What does the gamma subunit do?

Answer 12

It extends from the F1 head through the central stalk, making contact with the Fo base.

Question 13

What is the function of the Fo portion?

Answer 13

It forms a proton channel, allowing protons to flow from the intermembrane space into the matrix.

Question 14

How does the number of c subunits in the Fo base vary?

Answer 14

E. coli and yeast have 10, chloroplasts have 14, and mammals have 8.

Question 15

What is the binding change mechanism of ATP formation?

Answer 15

It is a hypothesis proposed by Paul Boyer that explains how ATP synthase produces ATP using a proton electrochemical gradient by changing the binding affinity of the active site rather than directly phosphorylating ADP.

Question 16

Does ATP formation require direct energy input?

Answer 16

No, ADP and Pi spontaneously condense into ATP when bound to ATP synthase. Energy is needed to release ATP from the enzyme, not for the phosphorylation itself.

Question 17

What are the three conformations of the ATP synthase catalytic sites?

Answer 17

1. Loose (L) – Binds ADP and Pi loosely.
2. Tight (T) – Binds nucleotides tightly and catalyzes ATP formation.
3. Open (O) – Has low affinity and releases ATP.

Question 18

How do the catalytic sites function?

Answer 18

Each site cycles through L ? T ? O conformations in a synchronized manner, ensuring continuous ATP production.

Question 19

What is rotational catalysis?

Answer 19

The ? and ? subunits of ATP synthase form a hexagonal ring that rotates relative to the central stalk. This rotation, driven by proton flow through the Fo base, converts electrical energy into mechanical energy, which is then used to form chemical energy (ATP).

Question 20

What structural evidence supports Boyer’s binding change mechanism?

Answer 20

Structural studies, including cryo-electron microscopy and the 1994 atomic model by John Walker’s team, confirmed that the three catalytic sites of ATP synthase differ in conformation and nucleotide affinity. These sites correspond to the L (loose), T (tight), and O (open) states.

Question 21

How does the ? subunit contribute to ATP synthesis?

Answer 21

The ? subunit extends from the Fo sector into the F1 catalytic core, transmitting conformational changes. It is asymmetric and interacts differently with each ? subunit, sequentially driving them through the L, T, and O conformations as it rotates in 120° steps.

Question 22

What experimental evidence directly demonstrates that ATP synthase operates as a rotary motor?

Answer 22

In 1997, Masasuke Yoshida and colleagues attached a fluorescently labeled actin filament to the ? subunit of ATP synthase and observed it rotating like a microscopic propeller when ATP was hydrolyzed. Later, researchers forced the ? subunit to rotate using a magnetic bead and a revolving magnetic field, which successfully induced ATP synthesis.

Question 23

How many ATP molecules are produced per full rotation of the ? subunit?

Answer 23

Three ATP molecules are synthesized with each 360° rotation, as each ? subunit passes through the L, T, and O states.

Question 24

How does ATP synthase compare to other biological rotary machines?

Answer 24

Rotary mechanisms are rare in biology. The only other known biological rotary nanomachine is the bacterial flagellum.

Question 25

What potential applications do ATP synthase's rotary properties have in bioengineering?

Answer 25

Engineers are exploring the possibility of using ATP synthase to power nanoscale devices, potentially replacing electricity in delicate instruments with ATP-driven energy systems.

Question 26

What was the key question about the Fo portion of ATP synthase in 1997?

Answer 26

The key question was: What is the path taken by protons as they move through the Fo complex, and how does this movement lead to the synthesis of ATP?

Question 27

What structure was proposed for the c subunits in the Fo complex?

Answer 27

The c subunits were proposed to be assembled into a ring that resides within the lipid bilayer.

Question 28

How does the movement of protons through the Fo complex drive ATP synthesis?

Answer 28

The 'downhill' movement of protons through the membrane drives the rotation of the c subunit ring, which generates torque that drives the rotation of the attached ? subunit. This rotation leads to ATP synthesis and release by catalytic subunits in the F1 ring.

Question 29

What evidence confirmed the structure of the c subunits in the Fo complex?

Answer 29

Evidence from X-ray crystallography, atomic force microscopy, and high-resolution electron micrographs confirmed that the c subunits are organized into a ring and that the b and a subunits reside outside the c ring.

Question 30

How are the c subunits and ? subunit connected?

Answer 30

The c subunits are connected to the ? subunit through hydrophilic loops at the top of each c subunit, forming a binding site for the ? and ? subunits. This connection allows the rotation of the c ring to drive the rotation of the ? subunit.

Question 31

How does the rotation of the c subunit ring occur?

Answer 31

Protons move from the intermembrane space through the half-channels of the a subunit, binding to acidic residues on the c subunits, causing them to rotate. After each subunit completes a rotation, it releases the proton into the matrix and resets for the next proton.

Question 32

What is the role of the proton-motive force in driving the c ring's rotation?

Answer 32

The proton-motive force, which is an electrical potential difference across the membrane, creates a small electric field that exerts a force on the charged acidic residue of the c subunit, driving the rotational motion of the c ring.

Question 33

How does the number of protons translocated relate to ATP synthesis?

Answer 33

The number of protons translocated is equal to the number of subunits in the c ring. For example, if the c ring has 12 subunits, the translocation of 12 protons will result in a full 360° rotation of the c ring and ? subunit, leading to the synthesis and release of three ATP molecules.

Question 34

How does the number of c subunits in the ring affect ATP synthesis?

Answer 34

The number of subunits in the c ring affects the proton-to-ATP ratio. More or fewer subunits would change this ratio but can be accommodated within the model of proton-driven rotation.

Question 35

What is the primary source of energy for mitochondria aside from ATP synthesis?

Answer 35

The proton-motive force is the primary source of energy for mitochondria, unlike most organelles that rely primarily on ATP hydrolysis.

Question 36

How does the proton-motive force contribute to the uptake of ADP and Pi into the mitochondria?

Answer 36

The proton-motive force drives the uptake of ADP and inorganic phosphate (Pi) into the mitochondria in exchange for ATP and H+, respectively, via the adenine nucleotide translocase (ANT).

Question 37

What role does adenine nucleotide translocase (ANT) play in mitochondria?

Answer 37

ANT facilitates the exchange of ATP for ADP across the mitochondrial membrane, making ATP available for use by the rest of the cell.

Question 38

What other activities are powered by the proton-motive force during aerobic respiration?

Answer 38

The proton-motive force is involved in activities such as the uptake of calcium ions into the mitochondrion, mitochondrial fusion, and the import of specifically targeted polypeptides into the mitochondrion from the matrix.