Mitochondria and Plastids (2024/25) PDF

Mitochondria and plastids Dr Rich Boden BIOL131(Z): Cells: The Building Blocks of Life (2024/25) @bodenlab  mitochondria and plastids This lecture covers the roles and structures of mitochondria and other plastids, bot...

Mitochondria and plastids Dr Rich Boden BIOL131(Z): Cells: The Building Blocks of Life (2024/25) @bodenlab  mitochondria and plastids This lecture covers the roles and structures of mitochondria and other plastids, both photosynthetic plastids and the other types. Popular science books that may prove useful for widening your horizons in a fairly gentle way include: Lane N (2015) The vital question: why is life the way it is? Oxford University Press. Lane N (2005, revised 2018) Power, sex, suicide: mitochondria and the meaning of life. Oxford University Press. Lane N (2002) Oxygen: the molecule that made the world. Oxford University Press. Morton O (2009) Eating the sun: how plants power the planet. Fourth Estate.  mitochondria majority of the Eukarya have them – can be up to 25 % of the cell volume in non-phototrophic organisms but number in a cell is very variable – erythrocytes in Homo sapiens subsp. sapiens L. have none, hepatocyates have >2,000 per cell. some Eukarya have lost them – two key Metazoa: 1) the unicellular flagellate Monocercomonoides exilis PA 203 from feces of Chinchilla lanigera Bennett. Has none AT ALL – ferments amino acids instead (substrate-level phosphorylation). [Eukarya > “Excavata” > “Metamonada” > Preaxostyla > Oxymonadida > Polymastigidae] Karnkowska et al. (2016) Current Biol. 26: 1274-1284. 2) the multicellular myxosporean Henneguya zschokkei – found as a parasite in many Actinopterygii. Has no true mitochondria, but has mitochondria-like structures. [Eukarya > Metazoa > Cnidaria > Myxozoa > Bivalvulida > Myxobolidae] Yahalomi et al. (2020) Proc. Natl. Acad. Sci. 117: 5358-5363. mitochondria: what do they do? main roles site of the respiratory chain: occurs on the inner membrane, proton-motive force (Δp) develops in the intermembrane space (as a proton gradient) and is used to drive ATP biosynthesis by the H+- transporting two-sector ATPase (EC 7.1.2.2, aka ATP phosphohydrolase [H+-translocating]). Colloquially called “ATP synthase”, but this name isn’t specific enough – many enzymes can generate ATP! (cf. Respiratory Chain lecture). site of Krebs’ cycle: pyruvate produced in glycolytic pathways is translocated into the mitochondrial matrix by active transport and the link reaction converts this to acetyl-CoA (cf. Krebs’ cycle lecture). site of fermentation: if molecular oxygen is limiting, Krebs’ cycle halts and pyruvate is fermented into lactate to generate NADH (used to make NADPH for anabolism) – the only ATP produced is substrate-level phosphorylation in glycolytic pathways (cf. Glycolytic Pathways lecture). site of non-shivering thermogenesis: takes Δp and uncouples it from ATP biosynthesis, allowing protons to flow into matrix via thermogenin – the energy from the gradient is released as heat. Mainly occurs in brown adipose tissue (cf. Respiratory Chain lecture). site of calcium homeostasis: Ca2+ is used widely in signal transduction – mitochondria take up and release Ca2+ ions, acting as ‘storage vessels’ for them, keeping them in the matrix (cf. Cell Communication lecture). site of regulation of cell division: ATP and NADPH are needed to generate new biomass – when cells are dividing, mitochondrial production of these molecules regulates the speed of division (cf. Mitosis and Meiosis lecture). mitochondria: what do they do? other roles regulating apoptosis (cf. Life and Death lecture). biosynthesis of steroids (cf. Vitamins and Steroids lecture) biosynthesis of heme cofactors hormonal signalling (particularly with estrogens) Remember, they divide by binary fission – if one is damaged at mtDNA level, that damage will appear in all descendant cells!  mitochondria: structures inner and outer membranes, separated by intermembrane space ribosomes Matrix matrix granules inner membrane thrown into cristae, which contain an extension of the intermembrane space, mitochondrial sometimes called the crista genomic DNA space. (mtDNA, L. fem. n. crista, crest on a circular) will be helmet. Plural: cristae in electrolucent areas mitochondrion from pancreas of Myotis lucifugus Le Conte matrix granules are typically phospholipids and calcium phosphates mitochondria: membranes outer membrane is 60-75 Å and is similar to the membrane of the cell the mitochondrion is in, in terms of protein-lipid ratio. outer membrane contains many porins and gated ion channels. outer membrane contains enzymes monoamine oxidase (EC 1.4.3.4) and long-chain- fatty-acid-CoA ligase (EC 6.2.1.3), among others. breaking the outer membrane kills the cell: proteins from the intermembrane space initiate apoptosis (cf. Life and Death in the Eukarya lecture). outer membrane is often associated to a region of endoplasmic reticulum termed the mitochondria-associated endoplasmic reticulum-membrane, which transfer lipids to the mitochondrion. inner membrane is site of the membrane proteins of the respiratory chain and the H+- transporting two-sector ATPase (EC 7.1.2.2). Also contains transport proteins to move things in and out of the matrix. inner membrane is rich in cardiolipin (diphosphatidylglycerol with usually C18:1 and C18:2 fatty acids) – helps maintain Δp: protons in the intermembrane space bind to the head of cardiolipin. intermembrane space is the site in which Δp develops – similar to cytoplasm but contains many more proteins e.g. cytochrome c. mitochondria: matrix about 60 % of the total soluble protein content of the mitochondrion is herein. contains enzymes of pyruvate oxidation and Krebs’ cycle, except for the membrane- bound succinate dehydrogenase (EC 1.3.5.1) which is on the inner membrane. contains mitochondrial ribosomes: 70S, comprising 50S and 30S subunits – former contains 23S and 5S rRNA, latter has16S rRNA. Compare cellular ribosomes in the Eukarya: 80S, comprising 60S and 40S subunits – former contains 28S, 5.8S and 5S rRNA, latter has 18S rRNA. contains mtDNA (mitochondrial genome): c.16.5 kbp in most Mammalia, but up to 80.9 kbp in Isarachnanthus nocturnus Hartog, of the Anthozoa. human mtDNA has 37 genes, encoding 11 respiratory chain enzyme subunits, 2 H+- transporting two-sector ATPase subunits, 2 ribosomal rRNAs, 22 tRNAs and the micropeptide humanin (24 aa, 2.7 kDa, a single alpha helix – may be cytoprotective in some way? It’s gene is actually a region of an rRNA gene, hence total is not 37!). human mtDNA has many genes that are associated with pathology if damaged (e.g. MT- CYB and MT-RNR1, Parkinson’s). mtDNA is passed down female line – Sykes B (2004) The Seven Daughters of Eve. Corgi. plastids phototrophy-associated plastids: chloroplasts – found in the Viridiplantae. Gr. masc. adj. χλωρός (khlōrós), the verdant green of new spring growth. rhodoplasts – found in the Rhodophyta. Gr. neut. n. ῥόδον (rhódon), a rose. cyanoplasts (cyanelles, muroplasts) – found in the Glaucophyta. Gr. masc. n. κῠ́ᾰνος (kúanos), dark blue enamel – has come to mean sky blue (cyan) over time. of these three plastids, there are basically different names when very young or old: etioplasts are immature chloroplasts/rhodoplasts etc that have not yet been exposed to light. Fr. v. étioler, to make pale in colour. gerontoplasts are senescing chloroplasts/rhodoplasts (etc) – once the grana have been unstacked, thylakoid membranes ruptured and plastoglobi form, the gerontoplast has formed. Gr. masc. n. γέρων (gérōn), an old man. chromoplasts synthesise and store pigments. Gr. neut. n. χρῶμᾰ (khrôma), colour, pigmentation. leucoplasts synthesise mononterpenes but can differentiate into four types: [Gr. masc. adj. λευκός (leukós), white] amyloplasts store starch and detect gravity (geotropism) [Gr. neut. n. ἄμῠλον (ámulon), starch] elaioplasts store fats. [Gr. neut. n. ἔλαιον (élaion), olive oil] proteinoplasts store proteins and sometimes modify them. tannosomes synthesise polyphenols and condensed tannins. chloroplasts: what do they do? site of phototrophic electron transport chain and thus where Δp is generated and used to drive ATP biosynthesis by the H+-transporting two-sector ATPase (EC 7.1.2.2) and where NADPH is synthesised by reverse electron transport (cf. Photolithoautotrophy lecture). plant immunity – plants don’t have true immune systems but chloroplasts can trigger apoptosis, the hypersensitive response etc to prevent pathogen colonisation. Chloroplasts also release salicylic acid, reactive oxygen species, jasmonate, methyl jasmonate etc that act as defence signals (cf. Cell Communication lecture). fatty-acid biosynthesis – all plant-cell fatty acids are made in chloroplasts. sugar and starch biosynthesis – chloroplasts generate hexoses from glyceraldehyde 3-phosphate, which are then assembled into sucrose (in the cytoplasm) or starches (amylose, amylopectin etc [Floridean starch in the Rhodophyta is NOT in rhodoplasts]). Starches are the main carbon store in plants and algae – the more CO2/DIC, the more starch (cf. Carbohydrates lecture). chloroplast structure (rhodoplasts look same!) stroma chloroplast DNA inner and outer membranes, separated by intermembrane space (cpDNA) and chloroplast ribosomes are not visible here. lamella or fret granum (dark patch) comprised These are also called of a stack of thylakoids stromal thylakoids. L. neut. n. granum, seed, grain. L. fem. n. lamella, thin Plural grana. plate of metal. Plural Thylakoid plural is thylakoids lamellae. (from Gr. masc. n. θῡ́λᾰκος (thū́lakos), sack or bag). plastoglobulus Each thylakoid is a bag: the starch granule space inside it is the lumen. etymologies to help! DO NOT learn by rote! -phyll, -phyte, -phyta etc from Gr. neut. n. φῠτόν (phutón), a plant, a tree. phyco-, fuci-, fuco-, -phyceae etc from Gr. neut. n. φῦκος (phûkos), seaweed and later L. masc. n. fucus, a red dye from seaweed. antho-, from Gr. neut. n. ᾰ ́νθος (ánthos), a flower, a bloom. bryo-, from Gr. neut. n. βρῠ́ον (brúon), moss. zea-, from Gr. fem. n. ζειᾱ́ (zeiā́), einkorn wheat, spelt – nowadays used for maize -bilin (aka –billin), porphyrin-based pigments related to those in the bile of the Mammalia -ene, an alkene or alkene-containing substance carot-, from L. fem. n. carota, a carrot. rhodo-, from Gr. neut. n. ῥόδον (rhódon), a rose. roseo-, from L. adj. roseus/rosea/roseum, rose-coloured. glauco-, from Gr. masc. adj. γλαυκός (glaukós), blue-green or blue-grey. ochro-, from Gr. masc. adj. ὠχρός (ōkhrós), pale yellow, yellow-brown. chloro-, from Gr. masc. adj. χλωρός (khlōrós), the verdant green of new spring growth. xantho-, from Gr. masc. adj. ξᾰνθός (xanthós), yellow. flavo-, from L. adj. flavus/flava/flavum, yellow. lutei-, from L. adj. luteus/lutea/luteum, the colour of saffron. chryseo-, from Gr. masc. adj. χρῡ́σεος (khrū́seos), golden. phaeo-, from Gr. masc. adj. φαιός (phaiós), grey. lyco-, from Gr. λύκοπερσικων (lúkopersikōn), wolf-peach (tomato!) chloroplasts vs rhodoplasts vs cyanoplasts chloroplasts of the Streptophyta use Chl a, Chl b, xanthophylls and carotenes. chloroplasts of the Chlorophyta use Chl a, Chl b, Chl c, xanthophylls and carotenes. chloroplasts of the Ochrophyta use Chl a, Chl c, xanthophylls and carotenes. rhodoplasts of the Rhodophyta use Chl a, xanthophylls, carotenes (in lower amounts than in chloroplasts) and phycobilins. cyanoplasts of the Glaucophyta use Chl a, xanthophylls, carotenes and phycobilins. We will pick this up in the Photolithoautotrophy lecture! chloroplast membranes outer membrane and inner membrane are each about 7 nm thick. outer membrane contains mainly phospholipids (about half of total) and galactolipids (half) and a small fraction of sulfolipids. inner membrane contains mostly galactolipids (80 %), then phospholipids, then sulfolipids. Galactolipids interact with light- harvesting systems. thylakoid membrane is similar to inner membrane with the addition of light harvesting pigments/photosystems etc. protons are translocated from the stroma to the thylakoid lumen to generate Δp. chloroplast stroma equivalent to bacterial cytoplasm or mitochondria matrix. slightly alkaline – dissolved inorganic carbon, bicarbonate etc. contains plastoglobuli – spherical lipid and protein ‘bubbles’ – increase in number during stress and grow as the chloroplast ages into a gerontoplast. Contain many lipids, vitamins and and pigments – mainly “debris” really. contains starch granules – composition varies. contain enzymes of the Calvin-Benson-Bassham cycle, thus the site of CO2 fixation into 3-phospoglyerate by ribulose 1,6-bisphosphate carboxylase/oxygenase (RuBisCO, EC 4.1.1.39). chloroplast ribosomes – similar to mitochondrial ones but less distantly evolved from the original “Cyanobacteria”. contains cpDNA (chloroplast genome): 120-170 kbp in most Viridiplantae – this encodes chloroplast ribosomes, tRNAs, electron transport chain (and allied proteins) and core enzymes of the Calvin-Benson-Bassham cycle, as well as chloroplast envelope transport proteins. chromoplasts formed from chloroplasts – cf. fruit ripening. reversible! We didn’t know that until fairly recently!!! mostly found in fruits and flowers. cpDNA is found in chromoplasts but with a high level Citrus limon (L.) Osbeck, of methylation [cf. epigenetics] showing ripening of fruit synthesise and store carotenoids, anthocyanins and other flavonoids. carotenoids containing oxygen e.g. zeaxanthin, lutein are xanthophylls – yellow in colour. carotenoids without oxygen e.g. lycopene, β-carotene are carotenes – mainly red or orange. anthocyanins are blue to violet flavonoids e.g. cyanidin Daucus carota L. taproots 3-glycoside. showing carotenes, xanthophylls and anthocyanins. other flavonoids include epigallocatechin 3-gallate (EGCg).  Summary: you should be able to 1. Sketch and label a mitochondrion showing all the key features. 2. Sketch and label a chloroplast, showing all the key features. 3. Give differences between inner and outer mitochondrial membranes, explaining why they exist – and the same for chloroplasts. 4. List all of the roles of mitochondria, explaining them in brief. 5. List all of the roles of chloroplasts, explaining them in brief. 6. Outline mtDNA and cpDNA, giving the key differences. 7. Give the key pigments for any given phototrophic plastid. 8. Outline ribosomal structures in the Eukarya versus in mitochondria/plastids. 9. Give the 3 plastids formed in the life cycle from new to old. 10. Give the 3 types of phototrophic plastid found. 11. Explain the roles of all of the non-phototrophic plastids. 12. Give examples of the pigments produced in chromoplasts.  Supplementary self-test 1. Give an example of a carotenoid that does not contain oxygen. 2. What is the role of the crista in mitochondria? 3. Where in mitochondria are ribosomes located? 4. What is the role of cardiolipin in mitochondrial membranes? 5. Name 3 types of non-phototrophy-associated plastid. 6. What are chromoplasts formed from? 7. What pigments to the cyanoplasts of the Glaucophyta use? 8. How big are mtDNA and cpDNA, typically? 9. What micropeptide is encoded by mtDNA and what does it do in vivo? 10. Name a defense-signalling compound released by chloroplasts in response to pathogen attack.  Supplementary self-test ANSWERS 1. Give an example of a carotenoid that does not contain oxygen. lycopene, α-carotene, β-carotene, γ- carotene, δ-carotene, ε-carotene 2. What is the role of the crista in mitochondria? to increase surface area of the inner membrane so that more respiratory chain/ATP biosynthesis proteins can fit into one mitochondrion. 3. Where in mitochondria are ribosomes located? matrix 4. What is the role of cardiolipin in mitochondrial membranes? The diphosphtatidylglycerol ‘head’ can bind two protons, helping to maintain Δp by reducing proton leakage. 5. Name 3 types of non-phototrophy-associated plastid. tannosome, amyloplast, elaioplast, proteinoplast 6. What are chromoplasts formed from? chloroplasts 7. What pigments to the cyanoplasts of the Glaucophyta use? Chl a, xanthophylls, carotenes and phycobilins 8. How big are mtDNA and cpDNA, typically? cpDNA 120-160 kpb, mtDNA 16.5-80.9 kbp. 9. What micropeptide is encoded by mtDNA and what does it do in vivo? humanin, has a role in cytoprotection 10. Name a defence-signalling compound released by chloroplasts in response to pathogen attack. jasmonate, methyl jasmonate, salicylic acid [can’t use ROS as they are not compounds!]