11 Bioenergetics and Metabolism

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11 Bioenergetics and Metabolism

• Chapter Outline
• Mitochondria
• Oxidative Phosphorylation
• Chloroplasts and Other Plastids
• Photosynthesis
• Peroxisomes

amyloplast
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Mitochondria, chloroplasts, peroxisomes

• Student learning outcomes
• Explain similarities, differences structure and
  function of mitochondria, chloroplast, peroxisome
• Explain process of transport of proteins to
  organelles
• signals on proteins, complexes that assist
• Explain metabolic functions of mitochondria,
  chloroplast membrane compartments, proton
  gradient and ATP
• Mitochondria and chloroplasts have genomes

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Figure 10.3 Overview of protein sorting

Fig. 10.3
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Introduction

• Generation of metabolic energy- major cell
  activity
• Mitochondria generate energy from breakdown of
  lipids and carbohydrates.
• Chloroplasts use sunlight energy to generate ATP
  and the reducing power needed to synthesize
  carbohydrates from CO2 and H2O.
• Peroxisomes contain metabolic enzymes
• fatty acid oxidation, generate peroxides,
  have catalase

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Mitochondria

• Mitochondria are surrounded by double membrane
• Outer membrane permeable to small molecules
• Inner membrane has numerous folds (cristae)
• extend into interior
  (matrix).

Fig. 11.1
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Fig 11.2 Metabolism in the matrix of mitochondria

• Matrix contains small genome (human 17 kb yeast
  80 kb)
• Enzymes for oxidative metabolism
• Pyruvate (from glycolysis) into mitochondria
  complete oxidation to CO2 yields most of energy
  (ATP) from glucose
• Enzymes of citric acid (Krebs) cycle - in
  mitochondrial matrix.
• Most of energy produced by oxidative
  phosphorylation,
• occurs on inner mitochondrial membrane
• (electron transport chain)

Fig. 11.2
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Mitochondria

• High-energy electrons from NADH and FADH2
  transferred through a membrane carriers membrane
  to molecular oxygen
• Energy of electrons converted to potential energy
  stored in a proton gradient, which drives ATP
  synthesis.
• Inner membrane has many proteins involved in
  oxidative metabolism and transport
• Inner membrane impermeable to most ions, small
  molecules

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Mitochondria

• Outer mitochondrial membrane highly permeable to
  small molecules
• Porins form channels for free diffusion of small
  molecules.
• Composition of intermembrane space similar to
  cytosol
• (with pH 7 matrix pH 8)
• Mitochondria can fuse,
• also can divide

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Mitochondria have DNA

• Genomes reflect endosymbiotic origin
• usually circular DNA molecules, multiple copies.
• encode only a few proteins (some oxidative
  phosphorylation).
• encode rRNAs and most tRNAs needed
• for translating protein-coding sequences
• Ribosomes are in matrix
• Some different codon usage

Table11.1
Human mtDNA 16-kb
Fig. 11.3
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Molecular Medicine 11.1 Diseases of
Mitochondria Lebers Hereditary Optic
Neuropathy LHON mutations in mitochondrial DNA

• Mutations in mitochondrial genes cause disease
• Lebers hereditary optic neuropathy, blindness
• mutations in mitochondrial genes
• components of
• electron transport chain

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Mitochondria

• Genes for many mitochondrial proteins in nucleus.
  
• Some genes transferred from prokaryotic ancestor
• Most proteins are synthesized on free cytosolic
  ribosomes, imported to mitochondria as complete
  polypeptides.
• Because of double-membrane structure of
  mitochondria, import of proteins is complex
• Matrix proteins are targeted by NH2-terminal
  sequences (presequences) removed after import

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Figure 11.4 Import of mitochondrial matrix
proteins

• Matrix proteins
• Membrane or free proteins
• Presequences target
• Tom receptors/ channels on outer membrane
  (translocase)
• Tim receptors on inner membrane
• Electrochemical gradient
• Hsp70 Chaperones
• MPP cleavage
• ATP hydrolysis
• Compare ER/Golgi

Fig. 11.4
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Figure 11.5 Binding cycle of an Hsp70 chaperone

• Presequence cleaved by matrix processing
  peptidase (MPP)
• Hsp70 chaperones
• facilitate folding.
• Similarity to signal
• peptidase for ER

Fig. 11.5
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Figure 11.6 Import of small molecule transport
proteins into the mitochondrial inner membrane

• Inner membrane proteins are small molecule
  transporters.
• multiple internal import signals,
• Hsp90 chaperone , plusTom70, translocates across
  channel.
• Intermembrane proteins escorted by mobile Tim22,
  Tiny Tims.
• Translocated through Tim22 internal
  stop-transfer signals causes exit insert inner
  membrane.

Fig. 11.6
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Figure 11.7 Sorting of proteins containing
presequences to different mitochondrial
compartments

• Both presequences, internal signal sequences.

• Translocated in Tom40.
• Some exit channel laterally,
• Some remain in intermembrane space
• Others transported back to intermembrane space
  
• Or inserted into inner membrane

Fig. 11.7
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Figure 11.8 Insertion of ß-barrel proteins into
the mitochondrial outer membrane

• Outer membrane proteins
• including Tom40 and ß-barrel proteins (e.g.,
  porins),

• Pass through Tom complex into intermembrane
  space.
• Carried by Tiny Tims to a SAM (sorting and
  assembly machinery) complex
• Inserted into outer membrane

Fig. 11.8
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Mitochondria

• Phospholipids are imported from cytosol.
• Phospholipid transfer proteins
• take phospholipids from ER membrane,
• transport them through cytosol,
• released at new membrane (e.g. mitochondria)
• Mitochondria catalyze
• synthesis of cardiolipin
• Phospholipid with
• four fatty acid chains..

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Figure 10.3 Overview of protein sorting

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The Mechanism of Oxidative Phosphorylation

• 2. Mechanism of Oxidative phosphorylation
• Electrons from NADH and FADH2 combine with O2
• Energy released from oxidation/reduction
  reactions
• drives ATP synthesis
• Electrons travel through electron transport
  chain
• Proteins on inner mitochondrial membrane
• Sets up proton gradient across membrane
• Intermembrane space has lower pH (more H)
• Chemiosmotic mechanism for synthesis of ATP
• Protons returning to matrix power ATP synthase.

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Fig 11.10 Transport of electrons from NADH

• Transfer of electrons from NADH
• Complex I,
• Coenzyme Q (ubiquinone)
• Complex III
• Cytochrome c
• Complex IV
• (cytochrome oxidase)
• to O2
• 3 H transported
• across membrane
• V is ATP synthase
• H reentry gives ATP

Fig. 11.10
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Fig 11.11 Transport of electrons from FADH2

• Transfer of electrons from FADH2
• Complex II (less energy)
• Coenzyme Q (ubiquinone)
• Complex III
• Cytochrome c
• Complex IV
• (cytochrome oxidase)
• to O2
• 3 H transported
• across membrane
• V is ATP synthase
• H reentry gives ATP

Fig. 11.11
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The Mechanism of Oxidative Phosphorylation

• Chemiosmotic coupling mechanism
• Couples electron transport to ATP generation.
• Electron transport coupled to transport of
  protons to intermembrane space
• Proton gradient
• across inner membrane
• Also electric potential
• Electrochemical
• gradient exists

Fig. 11.12
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Fig 11.13 Structure of ATP synthase

• ATP synthase
• Phospholipid bilayer impermeable to ions
• Protons cross through protein channel.
• Energy converted to ATP
• in complex V (ATP synthase)
• F0 is channel
• F1 rotates, makes ATP
• 4 protons to synthesize 1 ATP
• 1 NADH yields 3 ATP
• 1 FADH2 yields 2 ATP

Fig. 11.13
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Fig 11.14 Transport of metabolites across the
mitochondrial inner membrane

• Electrochemical gradient drives transport of
  small molecules into and out of mitochondria.
• ATP exported ADP and Pi brought in.
• Integral membrane protein transports 1 ADP in, 1
  ATP out
• Pyruvate exchanged for OH-

Fig. 11.14
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Chloroplasts and Other Plastids

• Chloroplasts organelles for photosynthesis
• Convert CO2 plus H2O to carbohydrates
• Synthesize amino acids, fatty acids, and lipids
  of their membranes.
• Similar to mitochondria
• generate metabolic energy,
• evolved by endosymbiosis,
• contain own genome
• replicate by division.

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Figure 11.15 Structure of a chloroplast

• Chloroplasts are larger and more complex
• double membrane chloroplast envelope.
• internal membrane system, thylakoid membrane,
• network of flattened discs (thylakoids),
• arranged in stacks (grana)
• 3 internal compartments
• intermembrane space
• stroma, mitochondrial matrix
• thylakoid lumen
• Electron transport, chemiosmotic
• generation of ATP in thylakoid membrane,
• not in intermembrane space

Fig. 11.15
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Fig 11.16 Chemiosmotic generation of ATP in
chloroplasts and mitochondria

• Comparison chemiosmotic mechanism locations

Fig. 11.16
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Chloroplasts and Other Plastids

• Chloroplast genome reflects evolutionary origins
  from photosynthetic bacteria.
• Circular DNA molecules, multiple copies,
• Encode RNAs, proteins for gene expression,
  photosynthesis

Rubisco catalyzes addition of CO2 to
ribulose-1,5-bisphosphate during the Calvin
cycle. Rubisco is critical enzyme for
photosynthesis,
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Chloroplasts and Other Plastids

• Proteins from cytosolic ribosomes imported after
  completion

• N-terminal transit peptide
• Guidance complex
• Proteolytic cleavage
• Toc complex
• Hsp70 chaperones
• Tic complex
• SPP stromal processing peptidase

Fig. 11.17
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Fig 11.18 Import of proteins into the thylakoid
lumen or membrane

• Thylakoid proteins have second signal sequence,
  (exposed after cleavage of transit peptide).
• 3 paths
• Chaperones
• charge
• SRP (signal
• recognition particle)

Fig. 11.18
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Chloroplasts and Other Plastids of Plants

• Plastids
• Double-membrane organelles including chloroplasts
• Plastids contain same genome, differ in
  structure and function.
• Chloroplasts unique internal thylakoid membrane
  and photosynthesis
• Classified by pigments

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Fig 11.19 Electron micrographs of chromoplasts
and amyloplasts

• Chloroplasts contain chlorophyll.
• Chromoplasts contain carotenoids result in
  yellow, orange, red colors of flowers and fruits
• Leucoplasts are nonpigmented - store energy
  sources in nonphotosynthetic tissues.
• Amyloplasts store starch
• Elaioplasts store lipids

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Chloroplasts and Other Plastids

• Plastids develop from proplastids,
• small undifferentiated organelles
• Mature plastids change.
• Chromoplasts from chloroplasts,
• in ripening fruit.
• Proplastids arrested at
• intermediate stage (etioplasts).
• In light, etioplasts develop
• into chloroplasts.

Fig. 11.20
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Photosynthesis

• 4. Photosynthesis
• ultimate source of energy for biological
  systems
• Light reactions
• energy from sunlight drives synthesis of ATP
  and NADPH, coupled to formation of O2 from H2O.
• Dark reactions
• ATP and NADPH drive glucose synthesis
• CO2 plus H2O form sugars

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Fig 11.22 Organization of a photocenter

• Sunlight absorbed by photosynthetic pigments -
  chlorophylls.
• Photocenters in thylakoid membrane have pigment
  molecules
• Absorption of light excites electron, converts
  light energy to potential chemical energy.
• Electrons transferred through membrane carrier
  chain, results in synthesis of ATP and NADPH

Fig. 11.22
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Fig 11.25 Electron transport and ATP synthesis
during photosynthesis

• Photosynthesis electron transport chain
• 4 complexes on thylakoid membrane.
• 2 photosystems (photosystems I and II) split H2O
• Cytochrome bf complex
• NADP reductase forms NADPH
• H gradient in thylakoid lumen
• ATP synthase

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Fig 11.27 The pathway of cyclic electron flow

• Cyclic electron flow uses electrons from
  Photosystem I only,
• generates extra ATP but not NADPH

Fig. 11.27
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Photosynthesis

• Summary photosynthesis
• Thylakoid membrane impermeable to protons, is
  permeable to other ions, particularly Mg2 and
  Cl
• Difference more than 3 pH units between stroma
  and thylakoid lumen ? lot of energy across
  membrane.
• Each pair of electrons gives 2 protons at
  photosystem II, 24 protons cytochrome bf
  complex.
• 4 protons for synthesis of 1 ATP each pair
  electrons yields 1 to 1.5 ATP.
• Cyclic electron flow yields 0.5 to 1 ATP per
  pair electrons.

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Peroxisomes

• Peroxisomes
• Single-membrane-enclosed organelles that contain
  diverse metabolic enzymes (peroxins)
• no genome

Fig. 11.28
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Peroxisomes

• Peroxisomes break down substrates by oxidative
  reactions, produce hydrogen peroxide.
• Peroxisomes contain catalase converts H2O2 to
  water or uses it to oxidize other organic
  compound.
• Peroxisomes synthesize lipids, amino acid
  lysine.
• In animal cells, cholesterol and dolichol are
  synthesized in peroxisomes and in ER.
• In liver, peroxisomes synthesize bile acids from
  cholesterol

Fig. 11.29
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Peroxisomes

• Peroxisome assembly
• Begins on rough ER 2 peroxins localize.
• Pex3/Pex19-containing vesicles bud off ER
• PTS1,2 signals target proteins
• from free ribosome to join peroxisome
• Signals recognized by
• receptors and protein channels
• Protein import, addition of lipids
• results in peroxisome growth, division.
• Enzyme content, metabolic activities
• of peroxisomes can change

Fig. 11.33
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Peroxisomes

• Diseases from deficiencies in peroxisomal
  enzymes, or failed import into peroxisome.
• Zellweger syndrome,
• lethal within first 10 years of life,
• results from mutations in at least
• 10 different genes affecting
• peroxisomal protein import.
• Peroxisome biogenesis disorders (PBD)
• part of leukodystrophies.
• Damage white matter of brain,
• affect metabolism in blood and tissues.

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• Review Questions
• What 2 properties of mitochondrial inner membrane
  give it unusually high metabolic activity?
• What roles do molecular chaperones play in
  mitochondrial protein import?
• Compare/ contrast import of proteins into
  mitochondria and into chloroplast membrane vs.
  cytoplasm
• 11. How are proteins targeted to peroxisomes?