Cell Structure & Function

What are the differences between diffusion, facilitated diffusion and active transport?

1) Diffusion: is the movement of molecules / ions from a region of higher to lower concentration. It may or may not occur across a semi permeable membrane. In diffusion there is no challenge involved as it is along the concentration gradient, but in active transport movement of molecules occur against concentration gradient ie; from lower to higher concentration. 2) For active transport, energy is vital for movement, in this case protein molecules function as molecular pumps to enable the cell accumulate glucose/ions, against concentration gradient. Here metabolic energy ATP is required. 3) Facilitated diffusion is a type of passive transport in which ions/molecules cross the semi permeable membrane because permeases present in the membrane facilitate the transport. Like simple diffusion facilitated diffusion doesn't require metabolic energy and simply occurs across the concentration gradient. 4) Osmosis: is movement of water from hypotonic solution (lower concentration) to hypertonic solution (higher concentration) through a semi permeable membrane. The cell membrane being permeable to water allows to and fro movement of water molecules along the concentration gradient.

What is the role of cholesterol in the plasma membrane/ Which organisms have cholesterol in the plasma membrane?

Cholesterol is a component of animal cell membranes, where it functions to maintain integrity and mechanical stability. It is absent in plant cells, as these plasma membranes are surrounded and supported by a rigid cell wall made of cellulose. Cholesterol is an amphipathic molecule (like phospholipids), meaning it has both hydrophilic and hydrophobic regions. Cholesterol's hydroxyl (-OH) group is hydrophilic and aligns towards the phosphate heads of phospholipids The remainder of the molecule (steroid ring and hydrocarbon tail) is hydrophobic and associates with the phospholipid tails.

What are the 3 major types of endocytosis? Provide a definition for each type.

Endocytosis involves bringing stuff from the extracellular fluid to the inside of the cell that is generally too large to cross the cell membrane on its own. This is a very important concept in cell biology. Phagocytosis In phagocytosis, the cell brings in solid particles. This is often referred to as cellular eating. Phagocytosis always makes me think of the cell like Pac-Man, eating his way along. In phagocytosis, a solid particle approaches the cell. This can include nutrients, proteins, and even bacteria. The cell membrane begins to indent. It keeps indenting and indenting until it surrounds the solid particle. Eventually, the cell membrane pinches off, forming a little bubble around the solid particle (shown in red in the image above). This bubble is called an endocytic vesicle, vacuole, or phagosome. The food particle is surrounded by a phospholipid bilayer (since it was pinched off from the cell membrane). This is an example of the fluidity of the cell membrane. Parts can pinch off, and no harm is done. The solid particle is eventually digested (broken down) by the cell, and the waste products and remaining phospholipids are sent back to the cell surface. Pinocytosis The overall process of pinocytosis is really similar to phagocytosis. There's the same pinching in of the membrane, only this time it's around a liquid particle. Pinocytosis is often called cellular drinking. To remember that pinocytosis is cellular drinking, I think of piña coladas. Piña coladas are drinks, and pino sounds like piña. Receptor-Mediated Endocytosis Luckily, receptor-mediated endocytosis (RME) isn't too different from phagocytosis and pinocytosis. The difference, though, is that RME is a much more specific process. There are receptors on the outside of the cell membrane specifically designed to recognize and bind to certain substances. Once this binding occurs, the cell membrane indents and it's the same old story as before. The key with RME is that the substance (called a ligand in this case) matches the receptors. The receptors don't bond to just any old thing. They recognize a specific ligand and bring it into the cell in vesicles formed from the membrane. In the picture above, the receptors are shown in green. These receptors are specific to the star-shaped ligand. They do not match up with the blue square ligands. This vesicle is still made of the cell membrane, but in addition to phospholipids it now includes the receptors, as shown in the image above.

Describe how eukaryotic proteins get delivered to the various cellular compartments after their synthesis on the rough ER.

In Eukaryotic cells, proteins are synthesized in the Rough Endoplasmic Reticulum(RER) and then transported to Golgi apparatus. in the Golgi apparatus the proteins are sorted before being sent to the lysosomes, secretory vesicles and the plasma membrane. Transportation of the proteins is necessitated by the vesicles which bud from one compartment and fuse to subsequent compartments.

What is the 'endosymbiotic theory'? Explain its relevance to the evolution of eukaryotes.

It is thought that life arose on earth around four billion years ago. The endosymbiotic theory states that some of the organelles in today's eukaryotic cells were once prokaryotic microbes. In this theory, the first eukaryotic cell was probably an amoeba-like cell that got nutrients by phagocytosis and contained a nucleus that formed when a piece of the cytoplasmic membrane pinched off around the chromosomes. Some of these amoeba-like organisms ingested prokaryotic cells that then survived within the organism and developed a symbiotic relationship. Mitochondria formed when bacteria capable of aerobic respiration were ingested; chloroplasts formed when photosynthetic bacteria were ingested. They eventually lost their cell wall and much of their DNA because they were not of benefit within the host cell. Mitochondria and chloroplasts cannot grow outside their host cell. Evidence for this is based on the following: 1. Chloroplasts are the same size as prokaryotic cells, divide by binary fission, and, like bacteria, have Fts proteins at their division plane. The mitochondria are the same size as prokaryotic cells, divide by binary fission, and the mitochondria of some protists have Fts homologs at their division plane. 2. Mitochondria and chloroplasts have their own DNA that is circular, not linear. 3. Mitochondria and chloroplasts have their own ribosomes that have 30S and 50S subunits, not 40S and 60S. 4. Several more primitive eukaryotic microbes, such as Giardia and Trichomonas have a nuclear membrane but no mitochondria. 5. Although evidence is less convincing, it is also possible that flagella and cilia may have come from spirochetes.

What are the roles of a cell wall? Which organisms have cell walls and what are their major components?

The cell wall is an outer protective membrane in many cells including plants, fungi, algae, and bacteria. Animal cells do not have a cell wall. The main functions of the cell wall are to provide structure, support, and protection for the cell. The cell wall in plants is composed mainly of cellulose and contains three layers in many plants. The three layers are the middle lamella, primary cell wall, and secondary cell wall. Bacterial cell walls are composed of peptidoglycan. Gram-positive bacteria have a thick peptidoglycan layer and gram-negative bacteria have a thin peptidoglycan layer.

Describe the term endomembrane system and write notes on its components

The endomembrane system (endo- = "within") is a group of membranes and organelles in eukaryotic cells that works together to modify, package, and transport lipids and proteins. It includes a variety of organelles, such as the nuclear envelope and lysosomes, which you may already know, and the endoplasmic reticulum and Golgi apparatus, which we will cover shortly. Although it's not technically inside the cell, the plasma membrane is also part of the endomembrane system. As we'll see, the plasma membrane interacts with the other endomembrane organelles, and it's the site where secreted proteins (like the pancreatic enzymes in the intro) are exported. Important note: the endomembrane system does not include mitochondria, chloroplasts, or peroxisomes. The endoplasmic reticulum The endoplasmic reticulum (ER) plays a key role in the modification of proteins and the synthesis of lipids. It consists of a network of membranous tubules and flattened sacs. The discs and tubules of the ER are hollow, and the space inside is called the lumen. Rough ER The rough endoplasmic reticulum (rough ER) gets its name from the bumpy ribosomes attached to its cytoplasmic surface. As these ribosomes make proteins, they feed the newly forming protein chains into the lumen. Some are transferred fully into the ER and float inside, while others are anchored in the membrane. Inside the ER, the proteins fold and undergo modifications, such as the addition of carbohydrate side chains. These modified proteins will be incorporated into cellular membranes—the membrane of the ER or those of other organelles—or secreted from the cell. If the modified proteins are not destined to stay in the ER, they will be packaged into vesicles, or small spheres of membrane that are used for transport, and shipped to the Golgi apparatus. The rough ER also makes phospholipids for other cellular membranes, which are transported when the vesicle forms. Since the rough ER helps modify proteins that will be secreted from the cell, cells whose job is to secrete large amounts of enzymes or other proteins, such as liver cells, have lots of rough ER. Smooth ER The smooth endoplasmic reticulum (smooth ER) is continuous with the rough ER but has few or no ribosomes on its cytoplasmic surface. Functions of the smooth ER include: Synthesis of carbohydrates, lipids, and steroid hormones Detoxification of medications and poisons Storage of calcium ions In muscle cells, a special type of smooth ER called the sarcoplasmic reticulum is responsible for storage of calcium ions which are needed to trigger the coordinated contractions of muscle fibers. There are also tiny "smooth" patches of ER found within the rough ER. These patches serve as exit sites for vesicles budding off from the rough ER and are called transitional ER. The Golgi apparatus When vesicles bud off from the ER, where do they go? Before reaching their final destination, the lipids and proteins in the transport vesicles need to be sorted, packaged, and tagged so that they wind up in the right place. This sorting, tagging, packaging, and distribution takes place in the Golgi apparatus (Golgi body), an organelle made up of flattened discs of membrane. The receiving side of the Golgi apparatus is called the cis face and the opposite side is called the trans face. Transport vesicles from the ER travel to the cis face, fuse with it, and empty their contents into the lumen of the Golgi apparatus. As proteins and lipids travel through the Golgi, they undergo further modifications. Short chains of sugar molecules might be added or removed, or phosphate groups attached as tags. Carbohydrate processing is shown in the diagram as the gain and loss of branches on the purple carbohydrate group attached to the protein. Finally, the modified proteins are sorted (based on markers such as amino acid sequences and chemical tags) and packaged into vesicles that bud from the trans face of the Golgi. Some of these vesicles deliver their contents to other parts of the cell where they will be used, such as the lysosome or vacuole. Others fuse with the plasma membrane, delivering membrane-anchored proteins that function there and releasing secreted proteins outside the cell. Cells that secrete many proteins—such as salivary gland cells that secrete digestive enzymes, or cells of the immune system that secrete antibodies—have many Golgi stacks. In plant cells, the Golgi apparatus also makes polysaccharides (long-chain carbohydrates), some of which are incorporated into the cell wall. Lysosomes The lysosome is an organelle that contains digestive enzymes and acts as the organelle-recycling facility of an animal cell. It breaks down old and unnecessary structures so their molecules can be reused. Lysosomes are part of the endomembrane system, and some vesicles that leave the Golgi are bound for the lysosome. Most of the proteins found in the membrane of a lysosome have an unusually large number of carbohydrate—sugar—groups attached to them. These sugar groups protect the membrane proteins by preventing the digestive enzymes in the interior of the lysosome from breaking them down. Lysosomes can also digest foreign particles that are brought into the cell from outside. As an example, let's consider a class of white blood cells called macrophages, which are part of the human immune system. In a process known as phagocytosis, a section of the macrophage's plasma membrane invaginates—folds inward—to engulf a pathogen, as shown below. The invaginated section, with the pathogen inside, pinches off from the plasma membrane to form a structure called a phagosome. The phagosome then fuses with a lysosome, forming a combined compartment where digestive enzymes destroy the pathogen. Vacuoles Plants cells are unique because they have a lysosome-like organelle called the vacuole. The large central vacuole stores water and wastes, isolates hazardous materials, and has enzymes that can break down macromolecules and cellular components, like those of a lysosome. Plant vacuoles also function in water balance and may be used to store compounds such as toxins and pigments (colored particles). Lysosomes vs. peroxisomes One point that can be confusing is the difference between lysosomes and peroxisomes. Both types of organelles are involved in breaking down molecules and neutralizing hazards to the cell. Also, both usually show up as small, round blobs in diagrams. However, the peroxisome is a different organelle with its own unique properties and role in the cell. It houses enzymes involved in oxidation reactions, which produce hydrogen peroxide (H2​O2​) as a by-product. The enzymes break down fatty acids and amino acids, and they also detoxify some substances that enter the body. For example, alcohol is detoxified by peroxisomes found in liver cells. Importantly, peroxisomes—unlike lysosomes—are not part of the endomembrane system. That means they don't receive vesicles from the Golgi apparatus.

What are the 3 major types of cytoskeletal structures? What are their major roles?

The filaments that comprise the cytoskeleton are so small that their existence was only discovered because of the greater resolving power of the electron microscope. Three major types of filaments make up the cytoskeleton: actin filaments, microtubules, and intermediate filaments. The cytoskeleton of eukaryotic cells is made of filamentous proteins, and it provides mechanical support to the cell and its cytoplasmic constituents. All cytoskeletons consist of three major classes of elements that differ in size and in protein composition. Microtubules are the largest type of filament, with a diameter of about 25 nanometers (nm), and they are composed of a protein called tubulin. Actin filaments are the smallest type, with a diameter of only about 6 nm, and they are made of a protein called actin. Intermediate filaments, as their name suggests, are mid-sized, with a diameter of about 10 nm. Unlike actin filaments and microtubules, intermediate filaments are constructed from a number of different subunit proteins. Tubulin contains two polypeptide subunits, and dimers of these subunits string together to make long strands called protofilaments. Thirteen protofilaments then come together to form the hollow, straw-shaped filaments of microtubules. Microtubules are ever-changing, with reactions constantly adding and subtracting tubulin dimers at both ends of the filament (Figure 1). The rates of change at either end are not balanced — one end grows more rapidly and is called the plus end, whereas the other end is known as the minus end. In cells, the minus ends of microtubules are anchored in structures called microtubule organizing centers (MTOCs). The primary MTOC in a cell is called the centrosome, and it is usually located adjacent to the nucleus. Microtubules tend to grow out from the centrosome to the plasma membrane. In nondividing cells, microtubule networks radiate out from the centrosome to provide the basic organization of the cytoplasm, including the positioning of organelles. The protein actin is abundant in all eukaryotic cells. It was first discovered in skeletal muscle, where actin filaments slide along filaments of another protein called myosin to make the cells contract. (In nonmuscle cells, actin filaments are less organized and myosin is much less prominent.) Actin filaments are made up of identical actin proteins arranged in a long spiral chain. Like microtubules, actin filaments have plus and minus ends, with more ATP-powered growth occurring at a filament's plus end. In many types of cells, networks of actin filaments are found beneath the cell cortex, which is the meshwork of membrane-associated proteins that supports and strengthens the plasma membrane. Such networks allow cells to hold — and move — specialized shapes, such as the brush border of microvilli. Actin filaments are also involved in cytokinesis and cell movement. Intermediate filaments come in several types, but they are generally strong and ropelike. Their functions are primarily mechanical and, as a class, intermediate filaments are less dynamic than actin filaments or microtubules. Intermediate filaments commonly work in tandem with microtubules, providing strength and support for the fragile tubulin structures. All cells have intermediate filaments, but the protein subunits of these structures vary. Some cells have multiple types of intermediate filaments, and some intermediate filaments are associated with specific cell types. For example, neurofilaments are found specifically in neurons (most prominently in the long axons of these cells), desmin filaments are found specifically in muscle cells, and keratins are found specifically in epithelial cells. Other intermediate filaments are distributed more widely. For example, vimentin filaments are found in a broad range of cell types and frequently colocalize with microtubules. Similarly, lamins are found in all cell types, where they form a meshwork that reinforces the inside of the nuclear membrane. Note that intermediate filaments are not polar in the way that actin or tubulin are.

How do SEM images differ from TEM images?

The main difference between SEM and TEM is that SEM creates an image by detecting reflected or knocked-off electrons, while TEM uses transmitted electrons (electrons that are passing through the sample) to create an image.

With respect to microscopes what do the following terms mean: magnification, resolution, contrast

The resolution of an optical microscope is defined as the shortest distance between two points on a specimen that can still be distinguished by the observer or camera system as separate entities. Magnification is the process of enlarging the apparent size, not physical size, of something. This enlargement is quantified by a calculated number also called "magnification". When this number is less than one, it refers to a reduction in size, sometimes called minification or de-magnification. Contrast is defined as the difference in light intensity between the image and the adjacent background relative to the overall background intensity.

Explain the different outcomes of proteins produced by ribosomes in the cytoplasm compared to proteins synthesized by ribosomes bound to the RER.

The secretory pathway refers to the endoplasmic reticulum, Golgi apparatus and the vesicles that travel in between them as well as the cell membrane and lysosomes. It's named 'secretory' for being the pathway by which the cell secretes proteins into the extracellular environment. But as usual, etymology only tells a fraction of the story. This pathway also processes proteins that will be membrane-bound (whether in the cellular membrane or in the ER or Golgi membranes themselves), as well as lysosomal enzymes, and also any proteins that will live their lives in the secretory pathway itself. It also does some things other than process proteins. The cytosol and the 'lumen' (the liquid that fills the secretory pathway) are different chemical environments, and they normally never mix. The cytosol is reductive (when you're in the cytosol, you keep meeting molecules that want to offer you electrons), and the ER, Golgi and extracellular environment are oxidative (molecules keep coming up to you asking for electrons). This makes for different protein-folding conditions: for instance, disulfide bonds usually only form in oxidative conditions. Moreover, different proteins may live only in the secretory pathway or only in the cytosol. The secretory pathway provides a route for the cell to handle things that might not be good to have in the cytoplasm, and/or are most useful when kept concentrated in a specialized compartment with their desired interacting partners. Hepatocytes (in the liver) sequester drugs and toxins in the smooth ER and break them down for excretion from the body there. The secretory pathway is not contiguous, but every movement between its components is in little bubbled-off microcosms of its own chemical world, called vesicles.

Compare and contrast the structures of: a. Smooth versus rough ER b. Chloroplasts versus mitochondria c. Inner versus outer membrane of mitochondria

a. The main difference between these two terminologies is that the Smooth Endoplasmic Reticulum is known for stocking lipids and proteins. It is not bounded by ribosomes. Whereas, the Rough Endoplasmic Reticulum is bounded by the ribosomes and also stores proteins. b. In mitochondria, ATP is produced as a result of oxidation and foodstuffs and is used as an energy source for metabolic processes. In chloroplasts, ATP is produced as a result of harvesting energy from light. In chloroplasts, ATP is used in the fixation of CO2 into sugars. c. The outer membrane has many protein-based pores that are big enough to allow the passage of ions and molecules as large as a small protein. In contrast, the inner membrane has much more restricted permeability, much like the plasma membrane of a cell.