1. 11 Bioenergetics and Metabolism
Chapter Outline:
Mitochondria
Oxidative Phosphorylation
Chloroplasts and Other Plastids
Photosynthesis
Peroxisomes
amyloplast

2. 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

3. Figure 10.3** Overview of protein sorting
Cell5e-Fig jpg
Fig. 10.3

4. Generation of metabolic energy- major cell activity
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

5. 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

6. 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
Cell5e-Fig jpg

7. 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

8. 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

9. Genomes reflect endosymbiotic origin:
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

10. Mutations in mitochondrial genes cause disease
Molecular Medicine Diseases of Mitochondria: Leber’s Hereditary Optic Neuropathy: LHON mutations in mitochondrial DNA
Mutations in mitochondrial genes cause disease
Leber’s hereditary optic neuropathy, blindness;
mutations in mitochondrial genes:
components of
electron transport chain
Cell5e-MM jpg

11. 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

12. Figure 11.4 Import of mitochondrial 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
Cell5e-Fig jpg
Fig. 11.4

13. 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
Cell5e-Fig jpg
Fig. 11.5

14. Inner membrane proteins are small molecule transporters.
Figure 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.
Cell5e-Fig jpg
Fig. 11.6

15. Both presequences, internal signal sequences.
Figure 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
Cell5e-Fig jpg
Fig. 11.7

16. Outer membrane proteins:
Figure Insertion of β-barrel proteins into the mitochondrial outer membrane
Outer membrane proteins:
including Tom40 and β-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
Cell5e-Fig jpg
Fig. 11.8

17. Phospholipids are imported from cytosol.
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..

18. Figure 10.3** Overview of protein sorting
Cell5e-Fig jpg

19. The 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.

20. 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
Cell5e-Fig R.jpg
Fig

21. 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
Cell5e-Fig jpg
Fig

22. 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

23. Fig 11.13 Structure of 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
Cell5e-Fig jpg
Fig

24. 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-
Cell5e-Fig jpg
Fig

25. 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.

26. 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
Cell5e-Fig jpg
Fig

27. **Comparison chemiosmotic mechanism locations
Fig Chemiosmotic generation of ATP in chloroplasts and mitochondria
**Comparison chemiosmotic mechanism locations
Cell5e-Fig jpg
Fig

28. 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,

29. 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

30. 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)
Cell5e-Fig jpg
Fig

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

32. 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
Cell5e-Fig jpg

33. 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

34. 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

35. 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
Cell5e-Fig jpg
Fig

36. 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
Cell5e-Fig jpg

37. 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
Cell5e-Fig jpg

38. 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, 2–4 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.

39. Peroxisomes
Peroxisomes:
Single-membrane-enclosed organelles that contain diverse metabolic enzymes (peroxins)
no genome
Fig

40. 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

41. Peroxisome assembly Peroxisomes
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

42. lethal within first 10 years of life,
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.

43. 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?