Mitochondria & Bioenergetics 1

University of Southampton - BIOL2056: Cell Biology: Mitochondria & Bioenergetics 1

  • Instructor: Prof Philip T.F. Williamson

  • Contact: P.T.Williamson@soton.ac.uk

Overview

  • Bioenergetics

    • Study focused on how cells utilize energy.

  • Mitochondria

    • Study the anatomy and structure of mitochondria.

  • Chemiosmotic Coupling

    • Principles of chemiosmotic coupling in energy utilization.

  • Electron Transport Chain

    • Mechanisms through which high-energy electrons generate electrochemical gradients, and detailed understanding of reaction complexes coupling electron transport to proton pumping.

  • ATP Generation

    • Function of ATPase in converting electrochemical gradients into ATP.

Sources of Cellular Energy

  • Sources of Energy for Cells:

    • Sugar

    • Fatty Acids

    • Amino Acids

    • Sunlight

    • Methane

    • Adenosine Triphosphate (ATP) as the energy currency.

  • Eukaryotes:

    • Use mitochondria and chloroplasts for energy.

  • Prokaryotes:

    • Utilize bacterial membranes.

Mitochondrial Anatomy

  • Structure:

    • Outer Membrane:

    • Encloses organelle; facilitates communication with cellular environment.

    • Inner Membrane:

    • Contains infoldings known as cristae which increase surface area for energy production.

    • Matrix:

    • Contains enzymes for metabolic processes like the TCA cycle and fatty acid oxidation.

    • Intermembrane Space:

    • Region between outer and inner membranes; participates in establishing proton gradients.

Origins of Mitochondria

  • Endosymbiotic Event:

    • Characterized by presence of:

    • Double Membrane: reflects evolutionary origins.

    • cDNA: Mitochondrial-specific circular DNA.

    • Transcription/Translation: Mitochondria possess unique transcription and translation machineries.

    • Human mitochondria:

    • Contains 16 kbp of DNA which encodes:

      • 13 respiratory chain proteins.

      • Large and small ribosomal RNAs (rRNA).

      • Specific transfer RNAs (tRNA) essential for translation support.

    • Mitochondria believed to derive from an ancestor of Rickettsia prowazekii, supporting the endosymbiotic theory.

Functions of Mitochondria

  • Reactions in Mitochondrial Matrix:

    • TCA Cycle:

    • Produces biosynthetic precursors for amino acids, porphyrins (e.g., heme and chlorophyll), and purines/pyrimidines.

    • Other metabolic processes include:

    • Beta-Oxidation of Fatty Acids.

    • Urea Cycle.

    • Amino Acid Synthesis.

    • Mitochondrial protein synthesis, producing essential metabolite NADH.

Mitochondrial Membranes

  • Composition:

    • Inner Mitochondrial Membrane (IMM):

    • Rich in proteins involved in the respiratory chain and ATP synthesis, optimized for energy generation and reaction localization.

    • Outer Mitochondrial Membrane (OMM):

    • Contains porins facilitating substrate passage and participates in signaling processes.

    • Structure similar to bacterial outer membranes but differing in lipid composition.

  • Membrane Composition Data:

    Lipid Class

    OMM (%)

    IMM (%)

    Phosphatidylcholine (PC)

    54

    40

    Phosphatidylethanolamine (PE)

    29

    34

    Phosphatidylinositol (PI)

    13

    5

    Phosphatidylserine (PS)

    2

    3

    Cardiolipin (CL)

    <1

    18

    Phosphatidic acid (PA)

    1

    -

Cardiolipin

  • Headgroup Structure:

    • Glycerol bridges two phosphatidic acids, forming an anionic lipid critical for function of cytochrome c.

    • Acyl Chains:

    • Composed of four acyl chains, contributing to the large volume occupied by each molecule.

Outer Mitochondrial Membrane (OMM) Functions

  • Acts as an interface between the cell and the endosymbiont.

  • Allows free passage of substrates necessary for energy generation.

  • Functions evolved towards a communication center for processes including:

    • Apoptosis

    • Mitophagy

    • Other cellular functions requiring energy.

Proteins in the OMM

  • Porins and Transport Proteins:

    • The OMM is permeable, rich in porins and helical membrane proteins, essential for transporting metabolites across the membrane.

  • Role of VDAC (Voltage Dependent Anion Channel):

    • Provides low energy barrier for exchange of ATP/ADP; lined with positive charges to ensure selectivity for ATP/ADP (anions).

  • Contact Sites:

    • Contain regions enriched in VDAC where OMM and IMM interface.

Mitochondrial Trafficking

  • Movement along Cytoskeletal Element:

    • Driven by motor proteins such as Kinesin and Dynein, linked to mitochondria by proteins Miro (a mitochondrial integral protein) and Milton (adaptor protein).

  • Regulation of Trafficking:

    • Mitochondrial position anchored to actin cytoskeleton (Myosin V) and microtubules (Syntaphilin).

Mitochondrial Contact Sites

  • Functions:

    • Facilitate lipid exchange between organelles.

    • Mediate Ca2+ signaling from the endoplasmic reticulum (ER) to mitochondria.

Inner Mitochondrial Membrane (IMM)

  • Primary Role in Energy Generation:

    • Contains proteins crucial for the respiratory chain.

  • Structural Features Enhancing Functionality:

    • Optimized for restricted diffusion and localization of key reactions.

    • Contains transporters necessary for substrate movement into the cytoplasm (e.g., ATP, Acetyl-CoA).

Electron Transfer Chain (ETC)

  • Functionality:

    • Facilitates high-energy electrons' transfer from the donor to the terminal receptor O2.

    • Couples electron transfer to proton transport across the bilayer, generating proton gradients.

F1F0-ATP Synthase

  • Structure and Function:

    • Comprised of:

    • Water-Soluble Head (F1): Responsible for ATP synthesis.

    • Transmembrane Domain (F0): Couples proton transport to the enzymatic reaction cycle, utilizing two half channels for transport linked to rotation.

ATP/ADP Shuttle (Adenine Nucleotide Translocator)

  • Mechanism of Function:

    • Stoichiometric exchange of ADP/ATP essential for energy availability within the cell.

    • Contains a nucleotide binding motif (RRRMMM) and operates as a dimer with two transmembrane domains (TMD).

    • ATP binding in the matrix initiates a conformational change optimizing transport.

Cristae Formation

  • Significance of Inner Membrane Geometry:

    • Cristae increase surface area for enzyme activity and localize reactions; essential for ETC efficiency.

    • Supports localized proton gradients and reduces diffusion of membrane proteins.

Summary of Key Points

  • Origins of mitochondria.

  • Comprehensive structure of mitochondria.

  • Role/functionality of mitochondrial compartments and membranes.

  • Mechanisms of location and transport within the cellular context.

Upcoming Topics for Next Week

  • Chemiosmotic coupling.

  • Further exploration of the electron transport chain.

  • In-depth study of ATP synthesis mechanisms via ATPase.

References

  • General:

    • Alberts, et al. Molecular Biology of the Cell.

    • Nicholls and Ferguson. Bioenergetics 4.

    • Berg and Stryer. Biochemistry.

  • Lecture Specific:

    • Davies et al. (2011 and 2012). PNAS.

    • Gray et al. (1999). Science.

    • Kuhlbrandt (2015). BMC Biology.

    • Schwarz (2013). Cold Spring Harbor Perspectives in Biology.

    • Philips and Voeltz (2016). Nature Reviews Molecular Cell Biology.

    • Laan (2016). Current Opinion in Cell Biology.

    • Pebay-Peyroula (2003). Nature.

    • Klingenberg (2008). Biochimica et Biophysica Acta.

    • Wagner et al. (2009). Current Opinions in Structural Biology.

    • Ujwal et al. (2008). PNAS.

  • Notes:

    • References typically consist of accessible review articles for further details on individual topics.

Overview of Bioenergetics

  • Bioenergetics Defined:

    • The study of energy transductions—the signaling and conversion of energy from one form to another within living organisms.

    • Focuses on how cells utilize energy to perform work, maintaining highly ordered structures against the second law of thermodynamics.

  • Mitochondria:

    • The central hub for eukaryotic energy metabolism, studying the anatomy and the compartmentalization of biochemical pathways.

  • Chemiosmotic Coupling:

    • The fundamental principle where the energy from electron transport is used to pump protons (H^+) across a membrane, creating an electrochemical gradient used to drive ATP synthesis.

  • Electron Transport Chain (ETC):

    • A series of redox reactions involving four major protein complexes (I, II, III, and IV) that facilitate the transfer of high-energy electrons to oxygen (O_2).

  • ATP Generation:

    • Direct focus on $F1F0$-ATPase, which acts as a molecular motor converting the proton motive force into chemical energy (ATP).

Sources of Cellular Energy

  • Energy Inputs:

    • Sugars (Glucose): Processed via glycolysis and subsequent mitochondrial oxidation.

    • Fatty Acids: Highly reduced carbon sources providing significant energy via $\beta$-oxidation.

    • Amino Acids: Carbon skeletons enter the TCA cycle at various points.

    • Sunlight: The ultimate source for phototrophic organisms (Chloroplasts).

    • Chemical Inorganics: Methane and other reduced compounds used by specific prokaryotes.

  • The Energy Currency:

    • Adenosine Triphosphate (ATP): High-energy phosphate bonds provide the delta $G$ necessary for biosynthetic reactions and mechanical work.

  • Evolutionary Context:

    • Eukaryotes: Rely on specialized organelles (mitochondria and chloroplasts).

    • Prokaryotes: Lack organelles; utilize the plasma membrane for respiratory and photosynthetic gradients.

Detailed Mitochondrial Anatomy

  1. Outer Mitochondrial Membrane (OMM):

    • Smooth, lipid-rich membrane containing large aqueous channels (porins).

  2. Inner Mitochondrial Membrane (IMM):

    • Highly impermeable and protein-rich (\sim 75\% protein by mass). Contains the machinery for the ETC and ATP synthesis.

    • Cristae: Extensive folding of the IMM to maximize surface area for respiratory chain components.

  3. Mitochondrial Matrix:

    • A concentrated aqueous solution of enzymes, mitochondrial DNA (mtDNA), ribosomes, and tRNAs. It is the site of the TCA cycle and fatty acid oxidation.

  4. Intermembrane Space (IMS):

    • Chemically equivalent to the cytosol regarding small molecules due to OMM permeability, but contains specific signaling proteins like Cytochrome c.

Origins and Genetics of Mitochondria

  • Endosymbiotic Theory:

    • Proposes that mitochondria originated from an $\alpha$-proteobacterium (related to Rickettsia prowazekii) engulfed by an ancestral archaeal/eukaryotic cell.

  • Genomic Characteristics:

    • Double Membrane: Inner membrane reflects the bacterial plasma membrane; outer membrane reflects the host's endosomal membrane.

    • Circular DNA (mtDNA): Humans possess 16,569 bp of circular DNA, which is maternally inherited.

    • Gene Content: Encodes 13 essential hydrophobic proteins of the respiratory chain, 2 rRNAs (12S and 16S), and 22 tRNAs.

    • Semiautonomous: Most mitochondrial proteins (over 1000) are encoded by the nuclear genome and imported into the organelle.

Metabolic Functions

  • TCA (Krebs) Cycle:

    • Converts Acetyl-CoA into CO2, generating $NADH$ and $FADH2$ as electron carriers.

    • Provides precursors for heme biosynthesis (succinyl-CoA) and amino acid synthesis ($\alpha$-ketoglutarate, oxaloacetate).

  • Metabolic Integration:

    • \beta-Oxidation: Breaking down fatty acyl-CoA into Acetyl-CoA.

    • Urea Cycle: Localized partially in the matrix (in liver cells) to detoxify ammonia.

    • Apoptosis: Mitochondria release pro-apoptotic factors (e.g., Cytochrome c) during programmed cell death.

Membrane Composition and Special Lipids

  • Cardiolipin (Diphosphatidylglycerol):

    • A unique four-tailed phospholipid found almost exclusively in the IMM.

    • Function: Stabilizes the structural integrity of the respiratory supercomplexes and traps protons near the membrane surface to enhance ATP synthesis efficiency.

  • Membrane Ratios:

    • OMM: High lipid-to-protein ratio, similar to the eukaryotic ER.

    • IMM: High protein-to-lipid ratio, reflecting its intense metabolic activity.

OMM Structure and VDAC

  • Porins (VDAC: Voltage-Dependent Anion Channel):

    • The most abundant protein in the OMM.

    • Facilitates the passage of molecules up to \sim 5000 Daltons.

    • Lined with positive charges to select for anions like $ATP^{4-}$ and $ADP^{3-}$.

Mitochondrial Dynamics and Trafficking

  • Mobility:

    • Mitochondria are not static; they move along microtubules to areas of high energy demand (e.g., neuronal synapses).

  • Molecular Motors:

    • Anterograde (to $+$ end): Kinesin motors.

    • Retrograde (to $-$ end): Dynein motors.

    • Adaptors: Miro (binds $Ca^{2+}$) and Milton link the motors to the mitochondrial surface.

  • Anchoring:

    • Syntaphilin acts as a "brake" to anchor mitochondria to microtubules in axons.

Mitochondrial Contact Sites

  • MAMs (Mitochondria-Associated Membranes):

    • Physical tethers between the OMM and the Endoplasmic Reticulum (ER).

    • Functions: Lipid synthesis (phosphatidylserine to phosphatidylethanolamine conversion), $Ca^{2+}$ signaling, and regulation of mitochondrial fission/fusion.

Inner Mitochondrial Membrane & Bioenergetics

  • Electron Transport Chain (ETC):

    • Transfer of electrons leads to the pumping of H^+ from the matrix to the intermembrane space.

    • Creates a Proton Motive Force ($Δ p$), consisting of a membrane potential ($\Delta \psi$) and a $pH$ gradient ($\Delta pH$).

  • F1F0-ATP Synthase:

    • $F_0$ (Stalk/Base): Proton-driven rotor embedded in the IMM.

    • $F_1$ (Head): Catalytic unit in the matrix that synthesizes ATP through a rotational mechanism.

  • ATP/ADP Shuttle (ANT):

    • The Adenine Nucleotide Translocase (ANT) is an antiporter that exports one $ATP^{4-}$ while importing one $ADP^{3-}$.

    • This exchange is electrogenic, driven by the membrane potential since $ATP^{4-}$ is more negative than $ADP^{3-}$.

Cristae Geometry and Efficiency

  • MICOS Complex:

    • Mitochondrial contact site and cristae organizing system. Regulates the formation of cristae junctions.

  • Purpose:

    • Compartmentalizes the IMS, creating "proton traps" at the cristae tips to drive ATP synthase more efficiently. Increases the density of respiratory enzymes per unit volume.