BL 424 Chapter 11: Bioenergetics and Metabolism: Mitochondria, Chloroplasts, Peroxisomes

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1 BL 424 Chapter 11: Bioenergetics and Metabolism: Mitochondria, Chloroplasts, Peroxisomes In addition to involvement in protein sorting and transport, organelles are specialized compartments for metabolism: Mitochondria and chloroplasts are devoted to production of ATP. Proteins for organelles are mostly synthesized on free ribosomes in the cytosol and then directly transported; mitochondria and chloroplasts also have their own organelle transcription and protein synthesis. Student Learning outcomes: Proteins are the active players in most cell processes. 1*. Explain concisely the similarities and differences in structure and function of these organelles. 2*. Explain the process of transport of proteins to mitochondria and chloroplasts; to appreciate the signals on proteins that identify their destinations.. 3*. Describe the diverse protein complexes that read the protein s signals and assist the transport: TOM, TIM, TOC, TIC complexes, chaperones, peptidases. 4*. Explain the essential metabolic functions of mitochondria and chloroplasts, (of oxidative phosphorylation and photosynthesis, respectively); note the importance of membrane compartments for formation of proton gradients and for function of the ATP synthase. 5. Describe the mitochondrial and chloroplast genomes, and that these genes are transcribed and translated within the organelle. 6. Recall that prokaryotes complete oxidative phosphorylation and photosynthesis by using their plasma membrane to generate the proton gradient. Important Figures: 2*, 4*, 5*, 6, 7*, 10*, 12, 13, 14, 15*, 16*, 17*, 18, 22, 25*, 33 Important Tables: 1, 2 1*. Mitochondria structure and organization. Mitochondria are critical for metabolic energy for generation of ATP from the breakdown of carbohydrates and fatty acids. Mitochondria have a double membrane structure: (Fig. 11.1) Matrix (interior) has enzymes of citric acid (TCA) cycle to oxidize Acetyl CoA to CO 2 ; also has DNA (Fig. 11.2) Inner membrane has numerous proteins involved in electron transport and oxidative phosphoyrlation (ATP). Outer membrane is permeable to small molecules Porins (channels) freely admit molecules < 1 kd. Recall that pyruvate is imported from cytosol, And converted to Acetyl CoA in matrix.

2 Mitochondria have DNA genomes: mostly circular, reflecting endosymbiotic origins. Humans 16-kb; yeast 80-kb; plants > 200 kb. Encode rrnas, trnas and some proteins involved in oxidative phosphorylation (about 13-32). Ribosomes are in the matrix; Translation in mitochondria has some special codon usage. Mutations of mitochondrial genes cause human disease: Mitochondria inherited from mother; Usually mix of normal and mutant affect tissues with large ATP requirement (eye, brain) LHON (Leber s Hereditary Optic Neuropathy) * Most mitochondrial proteins are encoded by the nuclear genome: (Figs. 4-7). About 1000 different proteins are synthesized on free ribosomes (cytoplasm) and then imported. Matrix proteins must traverse two membranes: Positively-charged N-terminal presequences (20-35 aa) target proteins for import; Presequences are removed by peptidase Matrix processing peptidase. Tom complex (translocase of outer membrane) includes receptors and channel proteins to to transport across first membrane. Tim complex (translocase of inner membrane) carries proteins into the matrix (Fig. 11.4). Chaperones assist the import, (Fig. 11.5, rachet) ATP hydrolysis powers the movement. Also electrical potential of membrane helps import +++ presequence into matrix (intermembrane space is more + charged H+ gradient) Proteins destined for insertion in membranes: (Fig. 11.6) Some transport proteins use Hsp90 and an Internal sequence for import and insertion. Lot of oxidative phosphorylation proteins in membranes Other proteins can have presequences and internal sequences (Fig. 11.7,8) to end up different places Phospholipids are carried to mitochondria from the ER by phospholipids transfer proteins. Ex. Cardiolipin (4 fatty acids) in inner mitochondrial membrane

3 2. Mechanism of oxidative phosphorylation. Most energy (ATP) from oxidative metabolism comes from the transfer of electrons from NADH and FADH 2 to a series of electron carriers in four complexes in the inner mitochondrial membrane. The transfer of electrons leads to proton transfer across the membrane (establishing a proton gradient electrochemical gradient (Fig *, 11.12*). Chemiosmotic coupling hypothesis (Peter Mitchell): (Fig ) A fifth protein complex, ATP synthase, couples ATP synthesis to the return of protons to the mitochondrial mateix (Fig ). 1 NADH -> 3ATP; 1 FADH 2 -> 2 ATP. The electrochemical, proton gradient also drives transport of ATP, ADP and other metabolites into and out of the Mitrochondrial matrix (Fig ). (Outer membrane is permeable to small molecules). 3. Chloroplasts and other plastids Chloroplasts are larger organelles (5-10 um; Fig ), and have 3 membranes: the double membrane defines the organelle; the stroma is equivalent to the mitochondrial matrix. The internal thylakoid membrane is site of electron transport and chemiosmotic ATP synthesis; enzymes are located on outer (stromal) surface. **Fig compares chemiosmotic generation of ATP for mitochondrial and chloroplast compartments. [Note: prokaryotes use their plasma membrane for chemiosmotic ATP synthesis for photosynthesis or oxidative phosphorylation.] Chloroplast genomes are kb, and contain about 150 genes; several plant chloroplast genomes have been sequenced. Encode 4 rrnas, 30 trnas and 21 ribosomal proteins, plus ~30 proteins for photosynthesis (Table 2). Some proteins are synthesized in chloroplast.

4 Import of proteins into chloroplast. About 95% of chloroplast proteins are encoded by nuclear genes; synthesized on free ribosomes, and imported; they must cross 2 or 3 membranes. The target sequence is an N-terminal ( aa) Transit peptide which is bound by guidance complex and directed to the Toc complex (Translocation outer membrane chloroplast (Fig ). Import requires Hsp70 chaperones, ATP, GTP hydrolysis. The transit peptide is not positively charged, but the intermembrane space (and stroma) do not differ in charge. Transit across the inner membrane uses Tic complex of receptors and channels; ATP is required; the Hsp100 chaperone assists. The transit peptide is cleaved in the stroma by Stromal processing peptidase (SPP). Proteins destined for the thylakoid lumen are first imported into the stroma, and then a second signal sequence is used for transport across the thylakoid membrane (Fig ). The N-terminal signals involve 3 different mechanisms: Chaperones, + charged, and signal recognition particle. *Other plant organelles (plastids) also have chloroplast genomes and two membranes, but serve other functions. Plastids develop from small proplastids. Chromoplasts lack chlorophyll but have other pigments (carotenoids); responsible for colors of flowers, vegetables. Leucoplasts nonpigmented, store energy sources: Amyloplasts store starch (ex. potatoes) Elaioplasts store lipids. Chloroplasts require light for development: In the dark, etioplasts with some internal membranes are an intermediate state (Fig ).

5 4. Photosynthesis converts energy from the sun to usable chemical energy form. Chlorophyll pigments organized in photocenters absorb light; electrons are excited and transferred to a series of carriers in the thylakoid membranes: (Fig ; Fig ) (photosystem II, photosystem I and cytochromes). Transfer of electrons is coupled to formation of proton gradient in the thylakoid lumen (ATP synthesis by ATP synthase in the stroma, with reduction of NADP+ to NADPH in stroma. Electrons are obtained by hydrolysis of water by photosystem II; photosystem I transfers electrons to NADP reductase (Fig ). [Cyclic electron flow uses electrons from Photosystem I only, and generates extra ATP but not NADPH (Fig ).] 5. Peroxisomes are small organelles with a single membrane that contain diverse enzymes for fatty acid oxidation, glyoxylate cycle and photo-respiration (Fig ). They often generate hydrogen peroxide; (Fig ) they contain catalase to decompose peroxides. Peroxisomes perform some biosynthesis of lipids (cholesterol and dolichol in animal cells are made here as well as in the ER). Peroxisome assembly begins in ER with formation of specific vesicles. Most peroxisome proteins are synthesized on free ribosomes and imported into nascent peroxisome (Fig ). Two types of signals target proteins to peroxisome: PTS1 is Ser-Lys-Leu at COOH end; PTS2 is 9-aa sequence at N-terminal. Signals are recognized by receptors and protein channels. Human disease occurs from mutations in peroxisomal enzymes or from defective import mechanisms. (ex. Zellweger syndrome is mutated PTS1 receptor) Lethal in 1 st 20 years of life) Review: Questions 1, 4, 5, 7, 8, 9, 11, 12. Consider the experimental basis of protein transport, and determination of signals. Compare the prokaryote model to that of organelles.

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