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Bio.203-6.TheCell
Molecular Biology Ch. 6 - A Tour of the Cell
| Question | Answer |
|---|---|
| Light microscope (LM) | Visible light is passed through the specimen and then through glass lenses. The lenses refract (bend) the light in such a way that the image of the specimen is magnified as it is projected into the eye or into a camera |
| Magnification | The ratio of an object’s image size to its real size. Light microscopes can magnify 1000x the actual size of the specimen. |
| Resolution | Measures the clarity of an image. It is the minimum distance two points can be separated and still be distinguished as two points. |
| Contrast | Accentuates differences in parts of the sample |
| Electron microscope (EM) | Focuses a beam of electrons through the specimen. Resolution is inversely related to the wavelength of the radiation a microscope uses for imaging. Electron beams have much shorter wavelengths than visible light. |
| Scanning electron microscope (SEM) (used to study topography) | The electron beam scans the surface of the sample, usually coated with a thin film of gold. The beam excited electrons on the surface and the secondary electrons are detected and translated into a 3D image. |
| Transmission electron microscope (TEM) | Used to study internal structures of cells. The TEM aims an electron beam through a very thin section of the specimen. The specimen is stained with atoms of heavy metals which attach to certain cellular structures. |
| Disadvantage of electron microscopy? | The methods used to prepare the specimen kills the cells |
| Cytology | The study of cell structure |
| Biochemistry | The study of chemical processes of cells |
| Cell fractionation | Taking cells apart and separating major organelles and other sub-cellular structures from one-another by means of a centrifuge. |
| In a prokaryotic cell, the DNA is concentrated in a region called … | The nucleoid |
| Cytoplasm | The interior of a cell between the nucleus and the plasma membrane. Note: in prokarya there is no nucleus, thus cytoplasm = everything within membrane. |
| Size: eukarya vs. prokarya | Eukarya are generally larger at 10-100 micrometers diameter. Prokarya are typically tiny bacteria at 1-5 micrometers diameter |
| Plasma membrane | Exists at the boundary of every cell. It functions as the selective barrier that allows passage of enough O2, nutrients, and wastes to service the entire cell. Surface area is critical and limits how large a cell can grow. |
| Organelles | Membrane enclosed structures within cells |
| Larger organisms don’t have larger cells; rather, they have more cells. Why is this? | Because surface area to volume ratio won’t permit them to grow very large |
| Function of microvilli in the intestine as related to cell size | Increase surface area without increasing volume |
| Embedded in the phospholipid bilayer of membranes … | Exists diverse proteins suited to the membrane’s functions. E.g., enzymes embedded in the membranes of mitochondria function in cellular respiration |
| Nucleus | Contains most of the genes in eukaryotic cells. It is the largest organelle in eukaryotes |
| Nuclear envelope | Encloses the nucleus in a double membrane (two lipid bilayers) |
| Surface of the nuclear envelope | It is perforated by pore structures. An intricate protein known as the *pore complex* lines each pore and controls the entry and exit of proteins and RNAs. |
| Nuclear lamina | The nuclear side of the nuclear envelope is lined by the nuclear lamina, a netlike array of protein filaments that maintains the shape of the nucleus by mechanically supporting the nuclear envelope. |
| Chromosomes | Structures that carry genetic information. Certain proteins help coil the DNA molecule of each chromosome, reducing its length and allowing it to fit into the nucleus. |
| The complex of DNA and proteins making up chromosomes is called | Chromatin |
| Number of chromosomes in humans | 46 in the nucleus of most cells, excluding sex cells which contain 23. |
| Nucleolus | Here is where ribosomal RNA (rRNA) is synthesized. Proteins are imported from the cytoplasm to assemble rRNA into sub-units of ribosomes. Then they’re taken through the pores into the cytoplasm where they’re assembled. |
| Ribosomes | Made up of rRNA and protein and are responsible for protein synthesis. Cells with high rates of protein synthesis will have many ribosomes (e.g. a pancreas cell has millions). Has two subunits that assembles in cytoplasm. |
| Ribosomes build proteins in two cytoplasmic locations… | 1. *Free ribosomes* are suspended in the cytosol, 2. *Bound ribosomes* are attached to the outside of the ER or nuclear envelope. Note: they’re both structurally identical and can alternate between roles. |
| Most of the proteins made by the free ribosomes function where? | Within the cytosol, e.g. enzymes that catalyze the first steps of sugar breakdown during cellular respiration and produced by free ribosomes. |
| Most of the proteins made by the bound ribosomes function where? | Proteins destined for insertion into membranes, for packaging within certain organelles such as lysosomes, or for export from the cell. |
| Endomembrane system: what does it include? | Includes the nuclear envelope, ER, golgi apparatus, lysosomes, various vesicles and vacuoles, and the plasma membrane |
| What tasks does the Endomembrane system carry out? | Synthesis of proteins, transport of proteins into membranes/organelles or out of the cell, metabolism and movement of lipids, and detoxification of poisons. |
| Vesicles | Tiny sacs made of membrane that the endomembrane system uses to transport membrane segments. These are budded off from the transitional ER. |
| Endoplasmic reticulum | Consists of a network of membranous tubules and sacs called cisternae. The ER membrane separates the internal compartment of the ER (ER lumen) from the cytosol. The lumen is continuous with the nuclear envelope. |
| How large is the ER? | Takes up half the total membrane in many eukaryotic cells. |
| Two distinct regions of the ER | Smooth ER: name derived from the lack of ribosomes on its surface. Rough ER: studded with ribosomes. Note: ribosomes are also attached to the cytoplasmic side of the nuclear envelope’s outer membrane |
| Function of smooth ER | Synthesis of lipids; detoxification of drugs; storage of calcium ions; metabolism of carbohydrates. |
| Smooth ER: synthesis of lipids | Enzymes of the smooth ER synthesize oils, phospholipids, and steroids |
| Smooth ER: detoxification of drugs | Enzymes add hydroxyl groups to drug molecules, making them more soluble and easy to flush from the body. Especially in the liver for detox of alcohol, barbiturates, etc. |
| Smooth ER: storage of calcium ions | Calcium is stored in the smooth ER lumen. When muscle cells are stimulated, calcium ions rush out into the cytosol and trigger contraction |
| Smooth ER: metabolism of carbohydrates | An example: an enzyme (glucose-6-phosphatase) in liver cells produced by the smooth ER removes phosphates from glucose phosphate molecules which yields pure glucose, which can then be metabolized. |
| Functions of rough ER | Creates proteins to be secreted outside the cell, e.g. insulin. Most secretory proteins are glycoproteins. The carbs are attached to them by enzymes built into the ER membrane. |
| Glycoproteins | Proteins that have carbohydrates covalently bonded to them |
| Secretory proteins | Proteins set to be secreted outside the cell |
| Aside from secretory protein synthesis, does the rough ER have any other function? | Yes, it is also a “membrane factory.” That is, it adds membrane proteins and phospholipids to itself. It also makes phospholipids from precursors in the cytosol. It will send them to other parts of endomembrane system if needed. |
| What happens to the secretory proteins? | They’re wrapped up into transport vesicles (from the transitional ER) and then sent to the Golgi apparatus |
| Transitional ER | Region at the boundary of the rough ER and the Golgi. Transport vesicles are responsible for the transfer of secretory proteins from this part of the rough ER to the Golgi system |
| Golgi apparatus | Essentially a warehouse receiving/shipping department with some manufacturing. Proteins from ER are modified/stored/shipped to other destinations. |
| Structure of Golgi apparatus | Consists of up to hundreds of stacks of cisternae. The membrane of the Golgi separates its internal space from cytosol. The cisternae are known as Golgi stacks. Vesicles are used for transport. |
| The two sides of a Golgi stack | Cis face and trans face. |
| Golgi stack: cis face | Located near the ER, it is the receiving department for vesicles sent from the ER. Vesicles budding from the ER can pass on its contents by fusing with the cis face. |
| Golgi stack: trans face | Shipping department. Gives rise to vesicles that pinch off and travel to other destinations. |
| How is Golgi cisternae different from ER cisternae? | They’re not physically connected |
| Before a Golgi stack dispatches its products via budding vesicles from the trans face, it … | Tags the proteins with molecular IDs such as phosphate groups which will bind to the proteins’ targets within the cell or at the plasma membrane. |
| Steps in transporting proteins from the ER to the trans face of the Golgi apparatus | 1. Vesicles bud from ER to Golgi, 2. Vesicles coalesce to form new cis Golgi cisternae, 3. Golgi, cisternae move in cis -> trans direction, 4. Vesicles form and leave Golgi, carrying specific products to other locations |
| During transport from cis -> trans, are proteins modified? | Yes, the golgi removes and replaces from sugar monomers from glycoproteins, producing a large variety of carbohydrates. Membrane phospholipids may also be altered in the Golgi. |
| What does the Golgi manufacture? | Some macromolecules including polysaccharides. They, like all other proteins, are disseminated via vesicles from the trans face |
| Lysosome | Membranous sac of hydrolytic enzymes that an animal cell uses to digest (hydrolyze) macromolecules. |
| What happens if enzymes escape lysosomes? | Lysosome enzymes are only active inside the acidic lysosome. If they leak, they won’t be very active in the neutral pH |
| Where are lysosomes’ enzymes made and why aren’t the enzymes digesting themselves? | ER and Golgi. The enzymes’ shape (folded protein configuration) protects them from being digestible by other lysosomes. |
| Describe the process of digestion by lysosomes | Organic matter is engulfed via phagocytosis. The particles are now contained within the newly formed “food vacuoles” in the cell. Lysosomes then fused with food vacuoles and begin digestion. |
| After the lysosome enzymes hydrolyze the contents of the food vacuoles, where are the remnants taken? | The products of the digestion are usable monomers which are excreted into the cytosol, e.g. simple sugars and amino acids. They can then be used as nutrients |
| What human cells carry out phagocytosis? | Macrophages: white blood cells that engulfs bacteria and other invaders. |
| Autophagy | (Pronounced aw-TOFF-uh-gee). Lysosomes recycle the cells own material, particularly damaged organelles |
| Tay-sachs disease | A certain type of lysosome (beta-N-acetylhexosaminidase; it digests a lipid found primarily in the nervous system) is impaired and can’t function in hydrolysis. The brain becomes impaired by the accumulation of lipids |
| 1. Vacuoles, 2. Food vacuoles, 3. Contractile vacuoles | 1. Large vesicles derived from the ER and Golgi apparatus. 2. Vacuoles filled with phagocytized polymers, 3. Exist in freshwater protists—they pump excess water out of the cell. |
| Small plant vacuoles | May contain reserves of important compounds such as seeds. Might also contain poisons to fend of animals. |
| Central vacuole (plants) | Develops after smaller vacuoles coalesce. It’s filled with “cell sap” which is a repository for inorganic ions such as Cl-. It enlarges as the plant absorbs water, allowing it to grow with minimal new cytoplasm. |
| Mitochondria | Sites of cellular respiration: metabolic processes that uses oxygen to generate ATP by extracting energy from sugars, fats, and other fuels. It is enveloped by double membranes. |
| Chloroplasts | Sites of photosynthesis in plants and algae. They absorb sunlight and use it to drive the synthesis of organic compounds such as sugars from CO2 and water. |
| Endosymbiont theory | Theory that mitochondria and plastids (e.g. chloroplasts) originated as prokaryotes engulfed by ancestral eukaryotes. They then evolved into a single organism. |
| Individuality of mitochondria/chloroplasts | They are somewhat autonomous organelles that grow and reproduce within the cell |
| Number of mitochondria in cells | Increases with the cell’s metabolic activity. |
| Cristae | While mitochondria’s outer membranes are smooth, their inner membrane is convoluted with infoldings called cristae. The folding gives the mitochondria more surface area. |
| Two internal compartments of the mitochondria | 1. Intermembrane space, 2. Mitochondrial matrix |
| Mitochondrial intermembrane space | One function of the intermembrane space is a repository for H+ to create a proton gradient |
| What is contained within the mitochondrial matrix? How large is a mitochondrion? | Mitochondrial DNA, ribosomes, and enzymes that make ATP. Size: 1-10 micrometers |
| Are mitochondria mobile? | Yes, they can be seen moving around microtubules, changing shapes, fusing, dividing, etc. |
| Why do plant cells have mitochondria? | Plants need mitochondria to convert the sugar (made from photosynthesis) to energy |
| Structure and contents of a chloroplast | Enveloped in a double membrane like mitochondria. Lens shaped at about 3-6 micrometers in length. They’re shape is changeable and mobile like mitochondria. They contain thylakoids, granum, stroma, and DNA/ribosomes |
| Chlorophyll | Green pigment found in chloroplasts |
| Thylakoids, granum and stroma | Thylakoids are flattened interconnected sacks of “machinery” to convert sunlight to energy. Each stack of thylakoids is called a granum. The fluid outside the thylakoids is the stroma (like the cytosol) |
| Plastids | Any of a class of small organelles in the cytoplasm of plant cells, containing pigment or food. E.g. chloroplasts, amyloplast, chromoplasts, etc. |
| Amyloplast | The colorless organelle that stores starch; particularly in roots. |
| Chromoplast | Has pigments that give fruits and flowers their orange and yellow hues |
| Peroxisome | A specialized metabolic compartment bounded by a single membrane. They contain enzymes that remove hydrogen atoms from substrates and transfer them to oxygen, thus producing H2O2, and then converts it to H2O |
| Function of peroxisomes | 1. Use O2 to break fatty acids down into smaller molecules that are transported to the mitochondria for cellular respiration. 2. Detox (in the liver) alcohol by transferring H from the poisons to O2. |
| Glyoxysomes | Specialized peroxisomes found in plant seeds. They have enzymes that convert fatty acids to sugar which the seedling uses as a source of energy until it can produce its own sugar by photosynthesis. |
| Cytoskeleton | A network of fibers that organizes structures and activities in the cell. It gives a cell its shape |
| Three structures of the cytoskeleton | 1. Microtubules (thickest), 2. Microfilaments (thinnest), 3. Intermediate filaments (middle) |
| How is the cytoskeleton of a cell different from animal skeleton? | It’s more dynamic. It can be quickly reassembled into a new location, changing the shape of a cell. |
| Cell motility | Movement; changes in a cell location and movements of parts of the cell. Requires motor proteins |
| Motor proteins | Outside cell: cilia/flagella allows for entire-cell movement. Inside cell: vesicles and other organelles use “feet” to “walk” along microtubules/microfilaments from ER to Golgi. Bends membrane to create vacuoles. |
| Microtubules | Hollow rods measuring about 25nm in diameter, from 200nm to 25micrometers in length. Constructed from a globular protein called tubulin |
| Tubulin | A dimer (has 2 subunits) consisting of two polypeptides: alpha-tubulin and beta-tubulin. Microtubules grow by adding tubulin dimers and can also be disassembled. |
| Can microtubules accumulate/dissociate rapidly from any direction? | The “plus end” of microtubules accumulate/release tubulin dimers more quickly than the other end. |
| Centrosome | A region where microtubules grow out from. It’s located near the nucleus. Known as the “microtubule organizing center”. |
| Centrioles | Within the centrosome is a pair of centrioles, each comprised of nine sets of triplet microtubules arranged in a ring. Before a cell divides, the centrioles replicate. Fungi/plant cells lack centrioles but have microtubules. |
| Cilia and flagella | Microtubule-containing extensions that project from some cells. Cilia: usually occur in large numbers on the cell surface. Flagella: same diameter but longer than cilia, but flagella are limited to only one or two per cell. |
| Beating patterns of cilia vs. flagella | Flagella undulate in the same direction of the flagellum’s axis, like the tail of a fish. Cilia undulations work more akin to oars, with alternating undulations in the direction perpendicular to the motion of the cell. |
| Internal structure of cilia/flagella | “9+2 pattern”: Used by motor cilia/flagella. Nine doublets of microtubules arranged in a ring. In the center are two single microtubules. “9+0 patter”: used by nonmotor cilia. The assemblies are anchored by basal body |
| Basal body | The part of the cilia/flagella that anchors it to the cell. It is a ring of triplets (as opposed to doublets) in the form of a 9+0 pattern. Note: recall the centrioles are also triplets |
| Radial spokes | Connections between the outer doublets and the two central microtubules |
| Nonmotile functions of cilia | Act as signal receiving antenna. Only one per cell in this case. Crucial to brain function. |
| Dyneins | They exist between microtubule doublets, connecting them to one another in a cross-linked pattern. Comprised of several polypeptides. With ATP is provided to them they contract and move the cilia/flagella. |
| Microfilaments (actin filaments) | Solid rods about 7nm in diameter (very small). They are also called *actin filaments* because they’re built from actin, a globular protein. Microfilaments are twisted double-chains of actin subunits. |
| Microtubules are _____ whereas microfilaments are _____ | Microtubules are compression (push) resisting, microfilaments are tension (pull) bearing |
| Microfilaments in muscle cells | Thousands are arranged parallel along the length of the muscle cell with *myosin* proteins in-between them (i.e. actin-myosin arrangement). Myosin (like dynein) contracts with ATP. |
| Microfilaments in cellular reproduction | The actin-myosin aggregates contract along the equatorial region of the cell membrane and form cleavage furrows that pinch the dividing animal cell into two daughter cells. |
| Actin-myosin in amoebas | Actin-myosin interactions cause contractions of the cell and pseudopia extensions (cellular extensions) to project outward. White blood cells exhibit a similar crawl. |
| Cytoplasmic streaming | A directed circular flow of cytosol (and thus cytoplasm) involving interactions of myosin and actin filaments that speeds the distribution of materials within cells. |
| Intermediate filaments | 8-12nm in diameter. Bear tension. Composed of keratin proteins which are permanent fixtures after death (e.g. skin cells filled with keratin). Nuclear lamina is made of intermediate filaments forming a cage for nucleus. |
| Cortical microfilaments | Microfilaments in the plasma membrane helping support cell’s shape. This network gives the outer cytoplasmic layer of a cell, called the cortex, the semisolid consistency of a gel as opposed to the inner fluid “sol” consistency |
| Cell wall | Extracellular structure of plant cells. Protects the cell, maintains shape, and prevents excessive uptake of water. Thicker than plasma membrane. Comprised of *microfibrils* made of cellulose. |
| How are microfibrils synthesized? | They are synthesized by an enzyme called cellulose synthase and secreted to extra-cellular space. |
| Primary cell wall | A young plant cell first secretes a relatively thin and flexible wall called the primary cell wall. |
| How do microfibrils affect growth? | Microfibrils in the cell cortex guide cellulose synthase as it synthesizes and deposits cellulose fibrils. Note the difference: not microtubules (proteins), but plants use microfibrils (cellulose). |
| Middle lamella | Between the primary cell walls of adjacent cells is the middle lamella, a thin layer rich in sticky polysaccharides called pectins. It glues adjacent cells together. |
| Secondary cell wall | Deposited in several laminated layers, has a strong and durable matrix that affords the cell protection and support. Wood consists mainly of secondary walls. |
| Extracellular matrix (ECM) | The stuff outside the plasma membrane in animal cells. Made up of glycoproteins and other carb-containing molecules. The most abundant glycoprotein is collagen which is embedded in proteoglycans |
| Collagen | Forms strong fibers outside the cell and accounts for 40% of protein inside the body. It’s the main component of connective tissue. |
| Proteoglycans | Heavily glycosylated proteins secreted by cells, forming large complexes in the ECM in which collagen and other proteins are embedded. Consists of a small core protein with many carb chains attached. |
| Fibronectin | Attaches the ECM to the integrins of the cell |
| Integrins | Cell surface receptor proteins to which fibronectins bind. Integrins are embedded in the plasma membrane. On the cytoplasmic side, they’re attached to microfilaments. |
| Why are integrins so significant? | They’re an important pathway through which the ECM communicates with the cell |
| Plasmodesmata | Channels between adjacent plant cells. Appear as perforations. They unify most of the plant into one living continuum. |
| Three types of cell junctions in animals | Tight junctions, gap junctions, desmosomes |
| Tight junctions | Plasma membranes are pressed very tightly together, bound together by specific proteins. Prevents fluid from passing through. E.g. tight junctions allow our skin to be water-proof. |
| Gap junctions | Similar to plasmodesmata. Channels are formed between cells consisting of membrane proteins that surround a pore through which ions, sugars, amino acids, and other small molecules may pass. E.g. CARDIAC MYOCYTES. |
| Desmosomes | They fasten cells together into strong sheets. Anchored by intermediate filaments of sturdy keratin proteins. E.g. “muscle tears” involve the rupture of desmosomes. |
| All cells (prokarya, eukarya) share certain basic features: | Plasma membrane, cytosol, ribosomes, chromosomes |
| In animal cells but not plant cells | Lysosomes, centrosomes/centrioles, flagella |
| In plant cells but not animal cells | Chloroplasts, central vacuole, cell wall, plasmodesmata |
| When the plant cell matures and stops growing, what happens to the cell wall? | Some plant cells simply secrete hard substances into its primary cell wall. Others add a secondary cell wall between the primary cell wall and plasma membrane |
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