Chapter 4 Notes PDF

4.1- Biologists use Microscopes and the Tools of Biochemistry to Study Cells Light microscopes were the first to be used and light passed through the lenses which was then refracted so the image was magnified Magnification is the ratio of an object's image size to its actual size...

4.1- Biologists use Microscopes and the Tools of Biochemistry to Study Cells Light microscopes were the first to be used and light passed through the lenses which was then refracted so the image was magnified Magnification is the ratio of an object's image size to its actual size Resolution is the measure of the clarity of the image Contrast is the difference in brightness and between the light and dark areas of an image The electron microscope focuses a beam of electrons through the specimen, resolution is inversely related to wavelength, ad electron beams have a much shorter wavelength than visible light, meaning electron microscopes have better resolution The scanning electron microscope is useful for the topography of a specimen, as it shows a 3D image of the specimen’s surface The transmission electron microscope is used to study the internal structures of cells Cell fractionation is when broken up cells are placed in a tube that is spun, which causes the components to settle into pellets when spun several times, enables scientists to prepare specific components in bulk and identify their functions 4.2- Eukaryotic Cells have Internal Membranes that Compartmentalize their Functions Prokaryotic- bacteria and archaea Eukaryotic- protists, fungi, plants, and animals All cells are bounded by a plasma membrane, subcellular units are suspended in cytosol, all contain chromosomes which carry genes in the form of DNA, all have ribosomes that make proteins according to instructions from the genes In eukaryotic cells, most of the DNA is in the nucleus which is bounded by a double membrane, generally much larger than prokaryotic cells In prokaryotic cells, the DNA is in the nucleoid, which is not membrane enclosed Interior of both is the cytoplasm and plasma membrane, which serves as a selective barrier that allows passage of enough oxygen and nutrients As a cell gets bigger, its surface area gets smaller; smaller objects have a greater ratio of surface area to volume A high ratio of surface area to volume is important in cells that exchange a lot of material; these cells have microvilli, which increase surface area without increasing volume The plasma membrane and organelle membranes play a part in the cells metabolism b/c enzymes are built into the membranes  4.3- The Eukaryotic Cell’s Genetic Instructions are Housed in the Nucleus and Carried Out by the Ribosomes The nucleus contains most of the genes in the eukaryotic cell (some are i mitochondria or chloroplasts), it is enclosed by the nuclear envelope, which separates it from the cytoplasm The nuclear envelope is a double membrane, each a lipid bilayer with proteins, has pores that are lined by the pore complex which plays an important role by regulating entry and exit of proteins, RNA’s, and complexes of macromolecules Besides the pores (openings), the nuclear side of the envelope is lined by the nuclear lamina which is a netlike array of protein filaments that maintain the shape of the nucleus DNA is organized into chromosomes which carry out genetic information The proteins on the DNA help coil the DNA to reduce the length to fit in the nucleus In the nucleolus, ribosomal RNA (rRNA) is synthesized from instructions in the DNA, proteins are assembled into with rRNA to into large and small subunits of ribosomes Ribosomes are made of rRNA and protein and carry out protein synthesis - Once mRNA molecules make it to the cytoplasm, ribosomes translate their genetic messages into the primary structure of a specific polypeptide - Cells that have a high rate of protein synthesis have many ribosomes as well as prominent nucleoli - Free ribosomes are suspended in the cytosol, while bound ribosomes are attached to the rough ER or nuclear envelope; they can alternate between being bound and free b/c they are structurally identical 4.4- The Endomembrane System Regulates Protein Traffic and Performs Metabolic Function in the Cell The endomembrane system is made up of the nuclear envelope, ER, golgi apparatus, lysosomes, vesicles, vacuoles, and the plasma membrane The endomembrane system synthesizes protein, transports protein, metabolism, movement of lipids, and detoxification The endoplasmic reticulum (ER) is an extensive network of membranes, consists of a network of membranous tubules and sacs called cisternae  Smooth ER - Functions in diverse metabolic processes, synthesis of lipids, metabolism of carbohydrates, detox of drugs, storage of calcium - Enzymes of the smooth ER are important to lipid synthesis - Steroids produced by the smooth ER include sex hormones and steroid hormones - Enzymes of the smooth ER detoxify drugs by adding hydroxyl groups to drug molecules to make them more soluble and easier to flush out Rough ER - Most secretory proteins are glycoproteins which have carbohydrates attached by enzymes built into the ER membrane - The rough ER is a membrane factory for the cell, it grows in place by adding membrane proteins and phospholipids to its own membrane - The ER membrane expands, and portions of it are transported to other components of the endomembrane system by transport vesicles Golgi Apparatus - Transport vesicles travel here after leaving to ER, the products from the ER are modified and stored, to then be shipped to other destinations - It is like a warehouse for receiving, sorting, shipping, and manufacturing - Consists of flattened, membranous sacs (cisternae) in stacks - The two sides of these stacks are referred to as the cis face (near the ER) and trans face which are respectively the shipping and receiving departments - Manufactures some macromolecules including polysaccharides - Molecular ID tags like phosphate groups aid in sorting Lysosome - Membranous sac of hydrolytic enzymes that are used to digest macromolecules - Hydrolytic enzymes and lysosomal membranes are made by the rough ER then transferred to the Golgi apparatus for processing - Phagocytosis is when amoebas and other unicellular eukaryotes eat by engulfing smaller organisms or food particles - Autophagy is when lysosomes use their hydrolytic enzymes to recycles the cell’s own organic material Vacuoles - Large vesicles derived from the ER and Golgi apparatus - Food vacuoles are formed by phagocytosis - Unicellular eukaryotes have contractile vacuoles that pump out excess water - Mature plant cells contain a central vacuole, which enlarges when it absorbs water, causing it to play a big role in growth 4.5- Mitochondria and Chloroplasts Change Energy from One Form to Another Mitochondria are the sites of cellular respiration in animals Chloroplasts are the sites of photosynthesis in plants and algae Mitochondria - Found in plants, animals, fungi, and most unicellular eukaryotes - The number of mitochondria a cell has correlates with its metabolic activity levels - Each of the mitochondria’s 2 membrane are a phospholipid bilayer with embedded proteins (outer membrane is smooth, but inner membrane is convoluted, caused by cristae) - The inner membrane divides the mitochondrion into 2 internal compartments, the intermembrane space, and the mitochondrial matrix which contains enzymes, mitochondrial DNA, and ribosomes - The enzyme that makes ATP is built into the inner membrane Chloroplasts - Contain chlorophyll along with enzymes that function in the photosynthetic production of sugar - Contents of the chloroplast are separates from the cytosol by an envelope with 2 membranes separated by narrow intermembrane space - Thylakoids are flattened, interconnected sacs; a stack of thylakoids is a granum; the fluid outside the thylakoids is the stroma which has the DNA, ribosomes, and enzymes - The chloroplasts is a member of organelles called plastids Peroxisomes - Specialized metabolic compartment bounded by a single membrane - Contain enzymes that remove hydrogen atoms from molecules and transfer them to oxygen, to produce hydrogen peroxide - Peroxisomes in the liver detoxify alcohol by transferring hydrogen from the poison to oxygen - They contain an enzyme that converts the hydrogen peroxide into water - Peroxisomes grow larger by incorporating proteins made in the cytosol and ER, and lipids made in the ER 4.6- The Cytoskeleton is a Network of Fibers that Organizes Structures and Activities in the Cell The cytoskeleton gives mechanical support to the cell to maintain its shape, and provides anchoring for many organelles; it is stabilized by a balance between opposing forces exerted by its elements Cell motility requires the interaction of the cytoskeleton with motor proteins The cytoskeleton manipulates the plasma membrane, bending it to form food vacuoles and more  Components of the cytoskeleton - Microtubules are the thickest; maintenance of cell shape, cell motility, chromosome movement in division, organelle movement - Intermediate filaments are coiled fibrous proteins; maintenance of cell shape, anchorage of nucleus and other organelles, formation of nuclear lamina - Microfilaments are the thinnest and made of actin (globular protein); maintenance of cell shape, changes in cell shape, muscle contraction, cell motility, cytoplasmic streaming in plant cells, cell division in animal cells Centrosomes are regions that are located near the nucleus and organize microtubules A pair of centrioles is in the centrosome and also organize microtubules The cilia and flagella are microtubule containing extensions that project from cells, propel many unicellular eukaryotic cells through water 4.7- Extracellular Components and Connections Between Cells Help Coordinate Cellular Activities Cell Wall (plant cells) - Maintains shape, protects, and prevents excessive uptake of water - Much thicker than the plasma membrane - The primary cell wall is what is first secreted by young plant cells, next is the middle lamella which has polysaccharides called pectins, some plant cells then add a secondary cell wall Extracellular Matrix (animal cells) - Made of glycoproteins (most abundant is collagen) and carbohydrate containing molecules secreted by the cells - Collagen fibers are embedded in a network of proteoglycans which have a small core protein with carbohydrate chains covalently attached - Integrins transmit signals between the ECM and cytoskeleton to integrate changes occurring outside and inside the cell Cell Junctions - Cell walls are perforated with plasmodesmata which unify most of a plant into one living continuum - Tight junctions in animal cells form continuous seals around the cells, making a barrier so that extracellular fluid is not leaked - Desmosomes fasten cells together into strong sheets, attach muscle cells to each other - Gap junctions provide cytoplasmic channels from one cell to another, necessary for communication between cells