Cellular Processes: Transport, Secretion, Endocytosis, Energy
Vesicle Budding
Vesicles that bud from membranes are usually coated vesicles that have a distinctive protein coat on their cytosolic surface. This protein coat shapes the vesicular membrane and allows it to interact with the targeted membrane to fuse. It also helps to capture molecules for onward transport.
Clathrin-Coated Vesicles
Clathrin-coated vesicles are vesicles coated by the protein clathrin, which bud from the Golgi complex on the outward secretory pathway and from the plasma membrane on the inward secretory pathway.
Each vesicle starts off as a clathrin-coated pit. Clathrin molecules assemble into a basket-like network on the cytosolic surface of the membrane, and this assembly process initiates the shaping of the membrane into a vesicle. Dynamin, a small GTP-binding protein, assembles as a ring around the neck of each deeply invaginated pit and, together with other proteins, causes the ring to constrict until the vesicle is pinched off from the membrane.
Clathrin-coated vesicles select their particular cargo by proteins called adaptins, which both secure the clathrin coat to the vesicle membrane and help capture specific cargo molecules by trapping the cargo receptors that bind them.
There are at least two types of adaptins: adaptin 1 binds Golgi complex cargo receptors, and adaptin 2 binds plasma membrane cargo receptors.
Vesicle Types and Destinations
- Clathrin-Coated Vesicles + Adaptin 1: Originating from the Golgi complex, destined for lysosomes via endosomes.
- Clathrin-Coated Vesicles + Adaptin 2: Originating from the plasma membrane, destined for endosomes.
- COPI-Coated Vesicles: Transport proteins from the cis-Golgi complex back to the rough ER, between Golgi compartments, and from the Golgi complex to the cell exterior.
- COPII-Coated Vesicles: Transport proteins from the rough endoplasmic reticulum to the Golgi complex.
Vesicle Fusion Mechanisms
Once a transport vesicle has reached its target, it must recognize and attach to the target organelle to fuse with the target membrane and unload the cargo. Each type of transport vesicle seems to display on its surface molecular markers that identify the vesicle according to its origin and cargo. The recognition of these markers is thought to involve a family of related transmembrane proteins called SNAREs. SNAREs of the vesicle (v-SNAREs) are recognized specifically by complementary SNAREs on the cytosolic surface of the target membrane (t-SNAREs). Each organelle and vesicle type is believed to carry a unique SNARE to ensure accurate fusion with the correct membrane.
Membrane fusion delivers the contents of the vesicle and also adds the vesicle membrane to the organelle’s membrane. Fusion does not always occur immediately after vesicle-organelle attachment but often awaits a specific molecular signal. Fusion requires a very close proximity between the vesicle and the organelles, and the displacement of water from the hydrophilic surface of the membrane. V-SNAREs and t-SNAREs are involved in this process by wrapping around each other after pairing, pulling the two membranes into close proximity.
Cellular Secretory Pathways
The secretory pathway starts with the biosynthesis of proteins on the ER membrane, which are moved to the Golgi complex via vesicles that fuse to the Golgi complex membrane (cis end). At the Golgi complex, proteins are sorted, modified, and packaged specifically in vesicles formed by budding from its membrane (trans end). The destination of these vesicles can be the plasma membrane or endosomes (a side branch) to eventually form a lysosome.
At the ER, most proteins are covalently modified. Disulfide bonds are formed to help stabilize the structure of the proteins against changes in pH and degradative enzymes. Many proteins are converted into glycoproteins by glycosylating enzymes of the ER, attaching to them the same 14-sugar oligosaccharide that undergoes a series of modifications in the ER and Golgi complex depending on the protein. The modified oligosaccharide can protect the protein against degradation, hold it in the ER until it is properly folded, or serve as a transport signal for appropriate packaging of the protein into a specific vesicle.
Proteins destined to function in the ER are retained there or returned from the Golgi complex by recognition of a terminal sequence of amino acids called the ER retention signal. However, many proteins are destined for other locations, and their exit from the ER is highly controlled to ensure protein quality. Incorrectly folded or assembled proteins are actively retained in the ER by binding to chaperone proteins that reside there until proper folding or assembly occurs; otherwise, they are ultimately degraded. Sometimes this quality control mechanism can be detrimental to the organism, as seen with cystic fibrosis disease. This disease causes a plasma membrane protein to be slightly misfolded. This misfolded protein is retained in the ER although it could still perform its function.
Proteins are further modified and sorted in the Golgi complex. Proteins from the ER are delivered via vesicles to the cis end where they fuse and travel through the Golgi complex via transport vesicles until the trans end where they exit. Both cis and trans Golgi networks are involved in protein sorting. At the cis end, proteins can move forward through the Golgi complex or return to the ER if they have an ER retention signal. At the trans end, proteins are sorted according to whether they are destined for lysosomes or the cell surface. Oligosaccharides of the proteins are further modified by enzymes present in the cisternae while they move along the Golgi complex.
Exocytosis Pathways
- Constitutive Exocytosis Pathway: Involves a continuous, steady flow of vesicles budding from the trans-Golgi network and fusing with the plasma membrane. This supplies new lipids and proteins, allowing membrane growth before cell division. It also transports proteins for secretion to the extracellular matrix or fluid, or to become peripheral membrane proteins. This non-selective pathway does not require a specific signal sequence and occurs in all eukaryotic cells.
- Regulated Exocytosis Pathway: Occurs only in cells specialized for secretion. These cells produce large quantities of specific products, stored in secretory vesicles for later release. Proteins traveling via this pathway have special surface properties causing them to aggregate under the ionic conditions (acidic pH and high Ca2+) prevalent in the trans-Golgi network. The aggregated proteins are then recognized and packaged into secretory vesicles, where they are concentrated and stored. These secretory vesicles accumulate near the plasma membrane, awaiting an extracellular signal to fuse and release their contents to the cell exterior.
Cellular Endocytic Pathways
By endocytosis, cells continually take in fluids, large and small molecules, and even large particles or other cells. The material ingested is progressively enclosed by a small portion of the plasma membrane that buds inward and pinches off, forming an endocytic vesicle. It is then delivered to the lysosomes, where it is digested.
Types of Endocytosis
Phagocytosis
Phagocytosis is the type of endocytosis by which phagocytic cells import large particles or other cells (e.g., pathogens, dead or damaged cells) by surrounding them with their plasma membrane. This occurs by the emission of pseudopods around the particle or cell until rounding it completely, forming a vesicle called a phagosome which contains the imported material. These phagosomes later fuse with lysosomes to digest the material. Phagocytosis is mediated by signaling; pseudopods are not emitted unless particles first bind to the phagocytic cell surface and activate specific surface receptors.
Pinocytosis
Pinocytosis is the type of endocytosis by which cells import fluids or small molecules present along with the fluid (dissolved or not) from the cell exterior by simple invagination of the plasma membrane. By clathrin-coated pits and later pinching off, vesicles which contain the fluid or molecules are formed, and they rapidly fuse with an endosome. Pinocytosis is indiscriminate; endocytic vesicles simply trap any molecules that happen to be present in the extracellular fluid and carry them into the cell.
Receptor-Mediated Endocytosis
Receptor-mediated endocytosis is a type of endocytosis by which cells take up specific macromolecules from the extracellular fluid. These macromolecules bind to complementary receptors on the cell’s surface and enter the cell as receptor-macromolecule complexes in clathrin-coated vesicles. This selective endocytosis provides a mechanism that increases the efficiency of internalization of specific molecules, taking large amounts of these molecules without taking in a correspondingly large volume of extracellular fluid. An example is cholesterol endocytosis.
Endosome Maturation & Sorting
Early endosomes mature gradually into late endosomes as the vesicles within them fuse with one another or with a preexisting late endosome. The interior of the endosome is kept acidic by an ATP-driven H+ pump in the membrane, which is crucial for the sorting of macromolecules that occurs in the endosome, causing many receptors to release their bound cargo. Possible routes of the receptors:
- Most are returned to the plasma membrane domain from which they originated.
- Some travel to lysosomes where they are degraded.
- Some proceed to a different domain of the plasma membrane.
Cellular Energy & Metabolism
The catabolism pathways include all the cellular reactions whose objective is to break down complex biomolecules into smaller molecules, generating useful energy for the cell. Additionally, it allows the cell to have these small molecules available, which will be used to synthesize cellular macromolecules and structures.
The anabolism pathways include the cellular mechanisms and reactions whose objective is the synthesis of cellular components from simpler molecules using the energy produced by the catabolic reactions.
These two sets of reactions constitute the metabolism of the cell.
Photosynthesis & Cellular Respiration
Photosynthesis is an anabolic reaction performed by plants, algae, and some bacteria that produces simple organic molecules (sugars) from inorganic molecules (commonly CO2 and H2O) using the energy of sunlight.
Cellular respiration is a catabolic reaction performed by most living organisms that breaks down organic molecules (commonly sugars) by oxidation into inorganic molecules (commonly CO2 and H2O), producing a controlled release of energy which is stored in the ATP molecule.
Photosynthesis and cellular respiration are complementary processes in the living world.
Cellular Energy Acquisition from Food
Enzymatic digestion breaks down the large polymeric molecules in food into their monomer subunits (proteins into amino acids, polysaccharides into sugars, and fats into fatty acids and glycerol) that enter the bloodstream. From the blood, the small organic molecules derived from food enter the cytosol of the cells, where their gradual oxidation begins.
Energy Storage in Organisms
Animals, for long-term storage, accumulate fatty acids as fat droplets composed of water-insoluble triacylglycerols in the cytoplasm of adipocytes, a specialized type of cell for that storage function. For shorter-term storage, sugar is stored in the form of a large branched polysaccharide, glycogen, which is found in the cytoplasm of many cells, especially in liver and muscle.
So, when cells need more ATP than they can generate from the food taken from the bloodstream, they break down glycogen. When energy needs are more acute, they use the fat reserves of the adipocytes.
Fat is far more important than glycogen as an energy store for animals. The oxidation of a gram of fat releases about twice as much energy as the oxidation of glycogen. An average adult human stores enough glycogen for only about a day of normal activities but enough fat to last for nearly a month.
Enzymes & Catalysis
Enzymes are molecules of proteinaceous nature that catalyze biological reactions, meaning they enable these reactions to occur at a suitable rate for sustaining life, all at ordinary temperatures. To do so, these enzymes bind to the substrate by the active site, forming a temporary complex that lowers the activation energy needed to transform that substrate to product, or in other words, to break some bonds and form new ones. The enzyme-substrate interaction depends on the three-dimensional structures of the substrate and enzyme active site, and it is stabilized by multiple weak bonds (e.g., electrostatic interactions, hydrophobic interactions, hydrogen bonds, van der Waals forces). During enzymatic reactions, the enzymes themselves remain unchanged. Enzymes in the cells are responsible for the control of biochemical pathways.
The oxidation of organic molecules is catalyzed by enzymes in small steps, through a sequence of reactions that allows useful energy to be stored.
The metabolic pathways are composed of a series of enzyme-catalyzed reactions.
Activated carriers are molecules that can store and transfer energy needed for metabolism, such as ATP. The energy produced in catabolism (energetically favorable reactions) is stored in chemical bonds of these molecules, which can be broken to recover that energy and use it to perform anabolism (energetically unfavorable reactions). The displacement of solutes down the electrochemical gradient is also a source of energy that is stored in the same way and can be used to move solutes against their electrochemical gradient (e.g., Na+/K+ pump, ATP synthase).
ATP: The Primary Activated Carrier
- ATP is synthesized in an energetically unfavorable phosphorylation reaction where a phosphate group is added to ADP (adenosine 5′-diphosphate).
- When required, ATP releases this energy packet through an energetically favorable hydrolysis to ADP and inorganic phosphate.
- The energetically favorable reaction of ATP hydrolysis is coupled to many otherwise unfavorable reactions, enabling the synthesis or activation of other molecules.
ATP can also be used to phosphorylate other molecules by transferring the phosphate group.
ATP & Biological Polymer Synthesis
- Macromolecules are synthesized from subunits (monomers) linked together by a condensation reaction.
- The breakdown of polymers occurs through the enzyme-catalyzed addition of water (hydrolysis).
- Hydrolysis reactions are energetically favorable, whereas biosynthetic reactions require an energy input and are more complex. (Condensation and hydrolysis are opposite reactions.)