Cell Structure Chapter 10

Cellular Respiration

• Harvests energy remaining in pyruvate and NADH from glycolysis

• Uses an external electron acceptor to oxidize substrates completely to CO2

• In aerobic respiration the terminal electron acceptor is oxygen and the reduced form is water. 

Where is Mitochondria found?

• All aerobic cells of eukaryotes

• Both chemotrophic and phototrophic cells

• Where there is the greatest need for ATP

Mitochondrial Structure

• Distinctive feature - both outer and inner membranes

  • Outer membrane contains porins

  • intermembrane space between inner and outer membrane

Inner Membrane

• Impermeable to most solutes

• 2 Separate Compartments:

  • Intermembrane space

  • Mitochondrial matrix (interior)

Cristae

Infoldings of the inner membrane meant to increase surface area and provide more space for electron transport to take place.

Note: Most proteins needed for respiration are imported into the mitochondria

Transit Sequences

Targeting signals located on the N terminal of a polypeptide

Transit peptidase

Enzymes that remove the transit sequence once the polypeptide has arrived

Transport Complexes

• Proteins are unfolded for transport into the mitochondria 

• Ports

  • TOM (translocase of the outer membrane)

  • TIM (translocase of the inner membrane)

Transit Sequence Receptors

• Component of transport complex that recognizes transit sequences

Chaperone Proteins

• Bind polypeptides targeted to the mitochondria to help maintain the unfolded state.

Import of Polypeptides into the Mitochondrial Matrix Mechanism

1. Hsp70 chaperone protein bind to polypeptide and help to unfold it

2. TOM transit sequence receptor binds the N-terminus of the polypeptide

3. Chaperone proteins released and ATP is hydrolyzed as polypeptide moves through the TOM and TIM pores

4. Transit Sequence removed by transit peptidase in the matrix as soon as the transit sequence enters matrix

5. Mitochondrial Hsp70 chaperone proteins bind polypeptide as it enters the matrix.

6. Often, mitochondrial Hsp60 proteins bind the polypeptide and assist in proper folding 

Citric Acid Cycle (TCA, Krebs Cycle)

Citrate is an important intermediate

Cleaving off carbons one at a time to release CO2 and making NADH

Overall Cycle

• 2 Carbons enter

• Release of 2 CO₂ and the regeneration of oxaloacetate

• Electrons are accepted by coenzymes

Bridging Reaction

• At the inner mitochondrial membrane a specific symporter transports pyruvate into the matrix along with a proton. 

• Then, pyruvate is converted into acetyl-CoA (By PDH), releasing CO2 and generating NADH

TCA Cycle

• Start with 3 carbon compound.

  • Cleave off one CO₂ in bridging reaction

  • Add other 2 to 4 C compound to make their cleavage easier

• 2 decarboxylations

• 3 NADH produced, 1 FADH2, and 1 GTP

• CoA is coenzyme and co-substrate in bridging reaction and in cycle.

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Structure of FAD and its Oxidation and Reduction

Citric Acid Cycle Summary

AcetylCOA + 3NAD⁺ + FAD + ADP + P_i → 2CO₂ + 3NADH + FADH₂ + COA - SH + ATP

Citric + Glycolysis + Pyruvate Decarboxylation

glucose + 10NAD⁺ + 2FAD + 4ADP + 4Pi → 6CO₂ + 10NADH + 2FADH₂ + 4 ATP

(Remainder of energy of the original glucose stored in NADH and FADH₂)

Allosteric Regulation for Cycle

Most of the control of the cycle involves regulation of 4 key enzymes by specific effector molecules.

• Effector molecules may be activators or inhibitors

Substrates and Products of TCA

Substrate: CoA, NAD+, FAD, ADP

Products: NADH, FADH₂, CO₂, ATP

Regulators and Activators

• NADH, ATP, and acetyl CoA are allosteric inhibitors of enzymes in this cycle (2 products)

• NAD+, ADP, and AMP each activate at least one regulator enzyme in this cycle (2 substrates)

Electron Transport

DEF: Transfer of electrons from reduced cofactors (NADH, FADH2 ) to oxygen

• fundamentally linked to ATP generation

Electron Transport Chain

DEF: a multistep process involving an ordered series of reversibly oxidized electron carriers functioning together

• Contains integral membrane proteins that are found in the inner mitochondrial membrane (or plasma membrane of bacteria)

Properties of the Respiratory Complexes

• Complexes I, III, IV are found in the inner mitochondrial membrane

• Complex II involved in succinate oxidation

• For each pair of electrons transported through complexes Ⅰ, Ⅲ, and Ⅳ, 10 protons are pumped from the matrix into the intermembrane space.

Complex 1

• Transfers electrons from NADH to CoQ and is called the NADH coenzyme Q oxidation complex (NADH dehydrogenase)

• Receives electrons from NADH → bound FMN cofactor → Fe-S center → Mobile pool of CoQ

• 2 electrons transferred, 4 protons pumped

Complex 2

• Transfers electron from Succinate → FAD. Electrons in FADH2 are transferred through Fe-S centers → CoQ

• Complex called Succinate dehydrogenase

• No protons pumped during this reaction

Complex 3

• 2 cytochromes are prominent components

• Accepts electrons from CoQ and transfers them to cytochrome C

• 2 Electrons transferred, 4 protons are pumped across the membrane. 

Complex 4

• Electrons transfer from cytochrome c to an Fe atom in the home A cofactor of cytochrome a then to cytochrome a₃. There are 2 copper atoms which each receive an electron. 

• 4 electrons are needed to reduce O₂ → H₂O

• 2 Protons pumped for each electron pair

Cytochrome C oxidase

Terminal oxidase, transferring electrons directly to oxygen

Cyanide and Azide ions are poisons because they block electron transport

Genes encoded by Mitochondria DNA

• Complex I, II, III, IV

• tRNAs

• Mitochondrial rRNA

Byproducts of Redox Reactions

• Complex I and III can result in incomplete reduction of oxygen

• Generates toxic superoxide anion O₂- or hydrogen peroxide H₂O₂ which age cells.

Electrochemical Proton Gradient

• Electron transport chain generates it

• Drives ATP synthesis

• Established by the directional pumping of protons across the membrane in which electron transport is occurring

• ATP synthesis is coupled to electron transport

Chemiosmotic coupling model

• Essential feature: link between electron transport and ATP formation is the electrochemical potential across a membrane 

  • Created by pumping of protons as electrons are transferred through complexes

    • Transfer of 2 electrons from NADH is accompanied by the pumping of a total of 10 protons

Number of ATP Generated 

2.5 - 3 ATP per NADH oxidation

1.5 - 2 ATP per FADH₂ oxidation

F₁F_o Complex

• F₁F_o ATPase generates ATP by coupling H+ transport with ATP synthesis

• Both complexes attached and embedded in inner membrane

• F_o acts as a proton translocator, the channel through which protons flow across the membrane 

• F_o provides channel for exergonic flow of protons

• F₁ carries out ATP synthesis powered by proton gradient

• Together they form a complete ATP SYNTHASE

F_o Structrure

• two b subunits and ten c subunits

• a and b subunits are static

• c subunits - form a ring that acts as a gear and can rotate

• a subunit - proton channel

• 2 b subunits - form the stator stalk which connects the F_oF₁ complexes

F₁ Structure

• three α and three β subunits, plus one δ, one γ, and one ε subunit

• ATP is synthesized by a ring of three αβ complexes.

• The δ subunit anchors the α₃β₃ catalytic ring to the b₂ stator stalk of F_o

• The mobile component of F1 is made up of the γ and ε subunits. They attach and move with the c subunits.

F₁F_o Function

Protons move through F_o channel → c₁₀ ring rotates spinning the γ subunit within the α₃β₃ catalytic ring → ATP synthesis by the catalytic ring

Binding Change Model

• proposed that each of the three β subunits of the F1 complex progresses through three different conformations

Three Conformations

• L (loose), binds ADP and P_i loosely

• T (tight), binds ADP and P_i tightly and catalyzes the formation of ATP

• O (open), little affinity for either substrates or product

Binding Change Structures

• Each β subunit passes through the O, L, and T conformations as the γ subunit rotates 360 degrees.

• In F_o, the 10 c subunits each have an aspartate residue with an ionic bond to an arginine residue on the immobile a subunit.

Binding Change Mechanism

• Proton taken in → neutralizes aspartate → disrupting ionic bond → rotating the C₁₀ ring (and y subunit) one tenth turn

• As the ring turns, the aspartate in the adjacent residue loses a proton and forms an ionic bond to arginine in the a subunit

• As 10 protons pass through the membrane via the a subunit, the ring goes through one complete rotation

Maximum ATP per Glucose

Note: Typically less

Why is it less?

• Typically 30-32 ATP/glucose

• Why?

  • H+ gradient used to exchange ADP and ATP into/out of the mitochondria

  • If NADH cannot enter matrix, an electron shuttle system will transport the electrons and H+ ions inward