Cell and Molecular Biology Fifth Edition CHAPTER 5 Part 1 Aerobic Respiration and the Mitochondrion Copyright © 2008 by John Wiley & Sons, Inc. Gerald Karp

5.1 Mitochondrial structure and function 1. Living fibroblast 2. TEM 3. Sperm midpiece 1-4μm, μm

1. Mitochondrial membranes The outer membrane is thought to be homologous to an outer membrane present as part of the cell wall of certain bacterial cells. The inner membrane is highly impermeable; all molecules and ions require special membrane transporters to gain entrance to the matrix.

2. The mitochondrial matrix Possess ribosomes, circular DNA to manufacture their own RNAs and proteins

5.2 Oxidative metabolism in the mitochondrion

An overview of carbohydrate metabolism in eukaryotic cells

Pyruvate + HS-CoA + NAD + → acetyl CoA + CO 2 + NADH + H + In matrix

1. The Tricarboxylic Acid (TCA) cycle Acetyl CoA + 2 H 2 O + FAD + 3 NAD + + GDP + P i → 2 CO 2 + FADH NADH + 3H + + GTP +HS-CoA

The glycerol phosphate shuttle Electrons are transferred from NADH to dihydroxyacetone phosphate (DHAP) to form glycerol 3-phosphate, which shuttles them into the mitochondrion. These electrons then reduce FAD at the inner membrane, forming FADH 2 which can transfer the electrons to a carrier of the electron-transport chain.

An overview of carbohydrate metabolism in eukaryotic cells

2. The importance of reduced coenzymes in the formation of ATP (Chemiosmosis) 1. High-energy electrons are passed from FADH2 or NADH to the first of a series of electron carriers in the electron transport chain. 2. The controlled movement of protons back across the membrane through an ATP-synthesizing enzyme provides the energy required to form ATP from ADP.

A summary of the process of oxidative phosphorylation

5.3 The role of mitochondria in the formation of ATP 1. Electron transport 2. Oxidation-reduction potentials 3. Types of electron carriers

1.Oxidation – reduction potential Oxidizing agents can be ranked in a series according to their affinity for electrons: the greater the affinity, the stronger the oxidizing agent.

Reducing agents can also be ranked according to their affinity for electrons: The lower the affinity, the stronger the reducing agent Reducing agents are ranked according to electron-transfer potential, such as NADH is strong reducing agent, whereas those with low electron- transfer potential such as H 2 O, are weak reducing agents.

Oxidizing and reducing agents occur as couples such as NAD+ and NADH. Strong reducing agents are coupled to weak oxidizing agents and vice versa. For example, in NAD + - NADH, NAD + is a weak oxidizing agent, in O 2 – H 2 O, O 2 is a strong oxidizing agent

The affinity of substances for electrons can be measured by instruments that detect voltage — oxidation-reduction (redox) potential.

2. Electron transport 1. Five of the nine reactions in matrix in Fig. 5.7 are catalyzed by dehydrogenases that transfer pairs of electrons from substrates to coenzymes, NADH and FADH 2 → electron- transport chain 2. NADH and FADH 2 dehydrogenase are located in the inner membrane of mitochondria.

3. Types of electron carriers Flavoproteins Cytochromes Ubiquinone Iron-sulfur proteins

Electron-transport complexes 1. Complexes I, II, III, IV ----Fixed in place 2. I, III, VI in which the transfer of electrons is accompanied by a major release of free energy. 2. Ubiquinone (lipid-soluble), cytochrome c (soluble protein in the intermembrane space)- ---move within or along the membrane

I, III, VI are described as proton pump which drive the production of ATP.

5.5 The mechinery for ATP formation 1. The structure of ATP synthase 2. The basis of ATP formation according to the binding change mechanism 3. Other roles for the proton-motive force in addition to ATP synthesis

RECALL THAT: 1. Enzymes do not affect the equilibrium constant of the reaction they catalyze 2. Enzymes are capable of catalyzing both the forward and reverse reactions

The structure of ATP synthase F 1 : head (90A) in matrix F0: basal region embedded in the inner membrane Mammalian liver has Ca copies of ATP synthase. Homology are found in the bacterial plasma membrane, inner membrane of mitochondria, and thylakoid membrane

2. The basis of ATP formation according to the binding change mechanism 1979 Paul Boyer (UCLA): published a hypothesis “ binding change mechanism ”

Using the proton gradient to drive the catalytic machinery: 1. What is the path taken by protons as they move through the F 0 complex? 2. How does this movement lead to the synthesis of ATP? 3. The role of the F 0 portion of ATP synthase

All of the following presumptions were confirmed by data collection between The c subunit of the F 0 base were assembled into a ring that resides within the lipid bilayer. 2. The c ring is physically bound to the γ subunit of the stalk. 3. The “downhill” movement of protons through the membrane drives the rotation of the ring of c subunit. 4. The rotation of the c ring of F 0 provides the twisting force that drives the rotation of the attached γ subunit, leading to the synthesis and release of ATP.

“ Seeing is beliving ” Masasuke Yoshida et al. at the Tokyo Institute Technology in Japan They devised an system to watch the enzyme catalyze the reverse reaction from the normally operating cell.

Only two biological structures are known that contain rotating parts 1. ATP synthase 2. Bacterial flagella 3. Both are described as rotary “ nanomachines ” 4. Invent nanoscale devices 5. Someday, human may be using ATP instead of electricity to power some of their most delicate instruments.

Rotation of the c ring drives rotation of the attached γ subunit H + movements drive the rotation of the c ring 1. Each “a” subunit has two half- channels that are physically separate 2. From intermembrane space into “a” subunit 4. From the middle of the “a” subunit into the matrix 3. Binding of the H+ to the carboxyl group of aspartic acid generates a major conformational change in the c subunit to rotate 30 o in a Counter- clockwise direction.

1. one H+ would remove the ring 30 o 2. In this case, the association/dissociation of 4 protons in the manner described would move the ring 120 o. 3. This would drive a corresponding rotation of the attached γsubunit 120 o and lead to release newly synthesized ATP. 4. The translocation of 12 protons would lead to the full 360 o rotation of the c ring and γ unit and synthesis of 3 molecules of ATP.

Other roles for the proton-motive force in addition to ATP synthesis