The algae chloroplasts have variable shapes, and their internal structures are very similar to cyanobacteria whose lamellar thylakoids are not stacked together. They are evidence of early evolution. The higher plant chloroplasts are ellipsoidal, and the internal structure is regular. They are composed of three parts: a double membrane envelope, thylakoids, and stroma. The electron microscope clearly reveals the chloroplast ultrastructure that can’t be distinguished by the optical microscope.
Plant Cell Chloroplast Double Membrane Envelope
Each membrane is between 6-8nm thick. The distance between them is 10-20nm. The outer membrane has pores that allow substances with a molecular weight below 10KDa to pass through. Unlike mitochondria, its inner membrane is smooth and lacks cristaes. It has stronger selective permeability because the it has more transport proteins. Many enzymes are also embedded here, especially those involved in lipid synthesis. The inner membrane is the main site for fatty acid synthesis in plants. Most fatty acids are synthesized into lipids in smooth ER.
The third membrane of chloroplast, thylakoid
There are many disc-shaped vesicles called thylakoids in the stroma. They derive from inward-folding inner membrane during chloroplast development. Thylakoids stack together like coins to form cylindrical grana that are maintained by van der Waals forces from membrane proteins. The lumens of all thylakoids are interconnected. There are about 5-30 thylakoids in a granum, sometimes even up to a hundred. One chloroplast contains about 40-100 grana. Tubular structures called stroma thylakoids, protrude from grana to connect neighbouring ones. This enclosed structure increases membrane area and separates thylakoid lumen from stroma. On average, each leaf has hundreds of square meters membrane for photosynthesis.
The thylakoid membrane consists of 50% protein and 50% lipid. Most lipids are glycolipids containing galactose, and only a small part is phospholipids. High content of polyunsaturated fatty acid is another unique feature. Pigments and proteins involved in photosynthesis are located on thylakoid membrane. These include Photosystem I and Photosystem II, chlorophyll, carotenoids, the electron transport chain, and ATP synthase. Chlorophyll gives leaves their green color. Light energy is passed through hundreds of chlorophylls and carotenoids to Photosystem II where a high-energy electron is excited. Then electron moves along the electron transport chain, and half energy is used to build a proton gradient inside thylakoid. It is similar in the previous step, Photosystem II re-excites the electron and stores half energy in NADPH.
Stroma
The space between envelope and thylakoids is filled with a jelly-like substance called stroma where Calvin cycle occurs. In addition to enzymes and various metabolites related to photosynthesis, the stroma also contains circular DNA and ribosomes. This means that chloroplasts can synthesize some proteins they need. However, chloroplasts still rely on nuclear DNA and other organelles in the cytoplasm to complete other proteins. Therefore, they are also known as semi-autonomous organelles.
Rubisco is the key enzyme in C3 cycle for fixing atmospheric carbon dioxide. All organic matter in biosphere is related to Rubisco directly or indirectly. The large subunit encoded by DNA is enzyme active site. The small subunit encoded by cell nucleus is responsible for regulating enzyme's activity and stabilizing its structure. Rubisco resembles a defective machine. At the current carbon dioxide concentration, it will mistakenly incorporate oxygen into pentose with 30% possibility. The flawed products are repaired in photorespiration that consumes extra energy. Furthermore, their extremely low efficiency means they can only fix 3 carbon dioxides per second. This is far below the average speed of enzymes catalyzing 1,000 substrates per second. The prevalent approach for compensation is the increased quantity, and more than half of proteins in stroma are Rubisco.
In addition to conducting C3 cycle in photosynthesis, the stroma is also a site for synthesis of fatty acids, carbohydrates and amino acids. Sometimes you can clearly see starch granules stay here temporarily under an electron microscope.