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Midterm

Bio_Midterm_Notes.pdf

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Department
Biology
Course Code
BIOL 1070
Professor
Anneke Olthof

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Chapter 1 and Lecture Notes ▯ Cell theory: o All organisms are composed of one ore more cells o The cell is the structural unit of life o Cells can arise only by division from a preexisting cell o All cells share similar basic properties ▯ Cells are highly complex and organized, the more complex a structure, the greater number of parts that must be in their proper place, the less tolerance of errors in the nature and interactions of the parts ad the more regulation or control that must be exerted to maintain the system ▯ Cells possess a genetic program and the means to use it. Organisms are built according to information encoded in a collection of genes ▯ The molecular structure of genes allows for changes in genetic information (mutations) that lead to variation among individuals, which is the basis of evolution ▯ Cells are capable of producing more of themselves ▯ Cells acquire and utilize energy. ▯ Cells carry out a variety of chemical reactions. Virtually all chemical changes that take place in cells require enzymes ▯ The sum  total  of  the  chemical  reactions  in  a  cell  represents  that  cell’s   metabolism ▯ Cells engage in mechanical activities ▯ Cells are able to respond to stimuli ▯ Cells are capable of self regulation (homeostasis) ▯ Cells evolve ▯ Two classes of cells known on earth: o Prokaryotic ▯ Bacteria ▯ Structurally simpler ▯ Have a nucleoid which is one big free circle of DNA (called a plasmid) ▯ Prokaryotes can produce more of themselves, they pick up new DNA from the environment o Eukaryotic ▯ Proteus, fungi, plants, animals ▯ Structurally more complex ▯ Have multiple forms of DNA (chromatin -> chromosomes). DNA is enveloped in membrane (nucleus) ▯ Undergo mitosis, which is the highly regulated production of daughter cells. Also undergoes meiosis, which is sexual reproduction of gametes ▯ Both types of cells are bounded by plasma membranes of similar construction that serve as a selectively permeable barrier between the living and nonliving worlds ▯ The genetic material of the prokaryotic cells is present in a nucleoid (a poorly demarcated region of the cell that lacks a boundary membrane to separate it from surrounding cytoplasm) and the genetic material of a eukaryotic cell is contained in a nucleus (a region bounded by a complex membranous structure called the nuclear envelope) ▯ Cells contain a large number of parts that need to be replicated and are organized with respect to time and space ▯ Viruses are non-cellular macromolecular packages that can function only within the living cells o Outside of cells of virus success as an inanimate particle (virion). Virions are comprised of a small amount of DNA or RNA and a protein capsule ▯ All viruses are obligatory intracellular parasites (they cannot reproduce unless present within a host cell) ▯ Viruses bind to a cell surface via specific proteins and enter into the cell, this defines the cell types the virus can infect and the host range ▯ Once inside the cell the virus then utilizes cellular machinery to synthesize new virus particles ▯ There are two types of viral infections: o Lytic: The virus arrests the normal synthetic activities of the host and redirects the cell to use its available materials to manufacture viral nucleic acids and proteins, which assemble into new virons. The infected cell ruptures (lyses) and releases a new generation of viral particles capable of infecting neighboring cells o Non-Lytic or Integrative: The infecting virus does not lead to the death of  the  host  cell  but  instead  inserts  its  DNA  into  the  DNA  of  the  host  cell’s   chromosomes. The integrated viral DNA is called a provirus. Chapter 4 and Lecture Notes ▯ Membrane functions: o Compartmentalization ▯ The plasma membrane encloses the content of the entire cell ▯ Membrane compartmentalization allows specialized activities to proceed without external interference and enables cellular activities to be regulated independently of one another o Scaffold for biochemical activities ▯ Membranes provide the cell with an extensive framework or scaffolding within which components can be ordered for effective interaction o Providing a selectively permeable membrane ▯ Membranes prevent the unrestricted exchange of molecules from one side to the other ▯ Membranes provide a means of communication between the compartments the separate ▯ Plasma membrane promotes the movement of select elements into and out of enclosed living space o Transporting solutes ▯ The plasma membrane contains the machinery for physically transporting substances from one side of the membrane to another, often from a region where the solute is present at low concentration into a region where that solute is present at much higher concentration ▯ The plasma membrane is also able to transport specific ions, thereby establishing ionic gradients across itself o Responding to external signals ▯ Plasma membrane plays a critical role in the response of a cell to external stimuli (signal transduction). Membranes possess receptors that combine with specific molecules (ligands) having a complementary structure. o Intercellular interaction ▯ The plasma membrane of multicellular organisms mediates the interactions between a cell and its neighbors. It allows cells the recognize and signal one another, to adhere when appropriate and to exchange materials and information o Energy Transduction (one type of energy is converted to another type) ▯ Photosynthesis ▯ Membranes are lipid-protein assemblies in which the components are held together in a thin sheet by non-covalent bonds ▯ The lipid bilayer serves primarily as a structural backbone of the membrane and provides the barrier that prevents random movements of water soluble materials into and out of the cell ▯ Membranes contain a wide diversity of lipid, all of which are amphipathic (contain both hydrophilic and hydrophobic regions) ▯ There are three main types of membrane lipids: o Phosphoglycerides-Most membrane lipids contain a phosphate group, which makes them phospholipids. Because most membrane phospholipids are built a=on a glycerol backbone they are called phosphoglycerides. Membrane glycerides are diglycerides (only two of the hydroxyl groups of the glycerol are esterified to fatty acids, the third is esterified to a hydrophilic phosphate group. Membrane phosphoglycerides have an additional group linked to the phosphate, with the group and the phosphate a highly water-soluble head group is formed. The fatty acyl chains make up the hydrophobic tails, they are made of unbranched hydrocarbons and that can be fully saturated (no double bonds), monounsaturated (one double bond) or polyunsaturated (multiple double bonds) o Sphingolipids-Are derivatives of sphingosine, an amino alcohol that contains a long hydrocarbon chain. Sphingolipids consist of sphingosine linked to a fatty acid by its amino group. Sphingolipids are similar in structure to phosphoglycerides and therefore are amphipathic. o Cholesterol-Are oriented with their small hydrophilic hydroxyl group toward the membrane surface and the remainder of the molecule embedded in the lipid bilayer. The hydrophobic rings of a cholesterol molecule are flat and rigid and they interfere with the movements of the fatty acid tails of the phospholipids ▯ Lipid composition can determine the physical state of the membrane and influence the activity of particular membrane proteins ▯ The components are mobile and they can interact ▯ All membrane share common properties: o 6 nm thick o Stable o Flexible o Capable self-assembly ▯ Membranes are asymmetrical (not exactly the same) o The two leaflets have distinct lipid compositions ▯ Liposomes-fluid filled spherical vesicles made from phospholipids ▯ There are three distinct classes of membrane proteins: o Integral proteins-penetrate the lipid bilayer. They are transmembrane proteins (pass entirely through the lipid bilayer and have domains that protrude from the extracellular and cytoplasmic sides of the membrane). o Peripheral proteins-located entirely outside the lipid bilayer on either side of the membrane and are associated with the membrane by noncovalent bonds o Lipid-anchored proteins-located outside the lipid bilayer on either side on the membrane and are linked to the membrane through a covalent bond with a lipid in the bilayer ▯ Most integral proteins function in the following capacities: o As receptors that bind specific substances at the membrane surface o As channels or transporters involved in the movement of ions and solutes across the membrane o As agents that transfer electrons during the process of photosynthesis and respiration ▯ Integral proteins are amphipathic ▯ Membrane fluidity is determined by: o The nature of lipids in the membrane ▯ Unsaturated lipids increased fluidity ▯ Saturated lipids reduce fluidity o Temperature ▯ Warming increases fluidity (liquid crystal state) ▯ Cooling decreases fluidity (crystalline gel state) ▯ Transition temperature-the temperature at which the lipids are converted from a liquid crystalline phase to a frozen crystalline gel ▯ The transition temperature of the bilayer depends on: ▯ The ability of the lipid molecules to be packed together which in turn depends on the lipids that make up the bilayer (saturated or un-saturated) ▯ Fatty acid chain length ▯ Cholesterol o Cholesterol ▯ Cholesterol alters the packing and flexibility of lipids ▯ If added to a liquid crystal membrane, fluidity will decrease ▯ If added to a crystalline gel membrane, fluidity will increase ▯ Membrane fluidity provides a compromise between a rigid, ordered structure in which mobility would be absent and a completely fluid nonviscous liquid in which the components of the membrane could not be oriented and structural organization and mechanical support would be lacking ▯ Fluidity allows for interactions to take place within the membrane ▯ Fluidity also plays a role in membrane assembly ▯ As fluidity increases so does permeability ▯ Local areas on the membrane have different amounts of fluidity ▯ To maintain cell fluidity cells respond to changing conditions by altering the types of phospholipids they are made of (homeostasis at the cellular level). They do this by: o Desaturation of lipids o Exchange of lipid chains ▯ A phospholipid can move laterally within the same leaflet quite easily but it takes much longer for a lipid to move from one leaflet to the other (transverse diffusion) ▯ In the preparation of artificial lipid bilayers, cholesterol and sphingolipids tend to self assemble into microdomains that are more gelated and highly ordered than surrounding regions consisting mainly of phosphoglycerides. Because of their distinctive physical properties the microdomains tend to float within the more fluid and disordered environment of the artificial bilayer. These patches are called lipid rafts. ▯ Lipid rafts are postulated to serve as floating platforms that concentrate particular proteins thereby organizing the membrane into functional compartments ▯ Means for the movement of substances through a membrane: o Passively by diffusion: ▯ Simple diffusion through the membrane: ▯ Based on both size and complexity ▯ Only very small uncharged molecules can confuse through the membrane unaided ▯ Move with the concentration gradient until equilibrium is met ▯ Diffusion through an aqueous, protein lined channel (ion channel): ▯ Small charge molecules (ions) ▯ Need to use channel because of hydrophobic tails ▯ Ion channels are formed by integral membrane proteins that enclose central aqueous pore ▯ Ion channels are highly selective in allowing only one particular type of ion to pass through the pore ▯ The diffusion of ions through a channel always goes from a state of high-energy to low-energy ▯ Often channels are gated ▯ Diffusion that is facilitated by a protein transporter ▯ Compound binds specifically to integral membrane protein called  “facilitative  transport” ▯ Change in shape of transporter allows compound to be released on other side of membrane ▯ Moves with concentration gradient o Actively by an energy-coupled transport process ▯ Active transport, which requires an energy-driven  protein  “pump”   capable of moving substances against a concentration gradient ▯ Partition coefficient-the ratio of a substances solubility in a nonpolar solvent ▯ Things that effect the rate of penetration (diffusion): o Polarity o Size o Charge ▯ There are three major types of gated (have a open or a closed conformation) ion channels: o Voltage gated channels-whose state depends on the difference in charge on the two sides of the membrane o Ligand (any substance/compound that binds to something) gated channels- whose state depends on the binding of a specific molecule (the ligand), which is usually not the solute that passes through the channel. Some ligand gated channels are opened or closed when a molecule binds to the outer surface of the channel others are opened or closed when a ligand binds to the inner surface of the channel o Mechano gated channels- whose state depends on mechanical forces (stretch tension) that are applied to the membrane Chapter 7 and Lecture Notes ▯ Epithelial tissue-lines the spaces within the body ▯ Connective tissue-consists largely of extracellular material ▯ Glycocalyx-the layer closely applied to the outer surface of the plasma membrane (cell coat). Mediates cell-cell and cell-substratum (the nonliving material or base on which an organism lives or grows) interactions, provides mechanical protection to cells, serves as a barrier to particles moving toward the plasma membrane and binds important regulatory factors that act on the cell surface ▯ Extracellular matrix (ECM)- an organized network of extracellular materials produced and secreted by the cells that is present beyond the immediate vicinity of the plasma membrane. ▯ Functions of the extracellular matrix: o Plays a key regulatory role in determining the shape and activities of the cell o Site for cell attachment o Physical support for cells o A substrate through which cells can move o Contains regulatory factors ▯ The extracellular matrix may take diverse forms in different tissues and organisms but it still tends to be composed of similar macromolecules. Unlike most proteins found inside the cell, which are compact and globular, the proteins in the extracellular space are typically extended and fibrous. ▯ Basement membranes provide mechanical support for the attached cell, generate signals that maintain cell survival, serve as a substratum for cell migration, separate adjacent tissues within an organ and act as a barrier to the passage of macromolecules. ▯ Cell walls: o Serve  collectively  as  a  type  of  “skeleton”  for  the  entire  plant o Protect the cell against damage from mechanical abrasions and pathogens o Mediate cell-cell interaction o Are a source of signals that alter the activities of the cells that it contacts ▯ Cellulose provides the fibrous component of the cell wall and proteins and pectin provide the matrix ▯ Cellulose molecules are organized into rod like microfibrils that confer rigidity on the cell wall and provide resistance pulling forces ▯ Cellulose molecules are polymerized at the cell surface ▯ Materials of the matrix are synthesized within the cytoplasm and carried to the cell surface in secretory vesicles ▯ The matrix of the cell wall is composed of three types of macromolecules: o Hemicelluloses are branched polysaccharides whose backbone consists of one sugar and side chains of other sugars. Hemicellulose molecules bind to the surface of cellulose microfibrils, cross linking them into a resilient structural network o Pectins are a heterogeneous class of negatively charged polysaccharides containing galacturonic acid. Pectins hold water and thus form an extensively hydrated gel that fills in the spaces between the fibrous elements o Proteins mediate dynamic activities (Ex. Cell growth). ▯ The percentage of these various materials in the cell wall are different depending on the type of plant ▯ Cell walls arise as a thin cell plate that forms between the plasma membranes of newly formed daughter cells following cell division Chapter 5 and Lecture Notes ▯ Anaerobes-organisms that captured and utilized energy by means of oxygen- independent metabolism (glycolysis and fermentation) ▯ Aerobes-dependent on oxygen ▯ Mitochondria within living cells are dynamic organelles capable of dramatic changes in shape ▯ Mitochondria can fuse or split in two ▯ When fusion becomes more frequent than fission the mitochondria tend to become more elongated and interconnected whereas a predominance of fission leads to the formation of more numerous and distinct mitochondria ▯ Mitochondria: o Play a role in generating the ATP that is used to run most of the cells energy requiring activities o Are the sites of synthesis of numerous substances o Play a vital role in the uptake and release of calcium ions, which are essential triggers for cellular activities o I am important role in regulating the Ca concentration of the cytosol ▯ The process of cell death which plays an enormous role in the life of all multicellular animals is also regulated to a large extent by the events that occur within the mitochondria ▯ The outer boundary of the mitochondria contains two membranes the outer mitochondrial membrane and the inner mitochondrial membrane ▯ The outer mitochondrial membrane completely encloses the mitochondria serving as its outer boundary, contains many enzymes with diverse metabolic functions. The outer mitochondrial membrane has porins which are large channels, when they are open the membrane is freely permeable ▯ The inner mitochondrial membrane is subdivided into two interconnected domains one of these domains called the inner boundary membrane lies just inside the outer mitochondrial membrane forming a double membrane outer envelope ▯ Inner boundary membrane is particularly rich in proteins responsible for the import of mitochondrial proteins ▯ The other domain of the inner mitochondrial membrane is present within the interior of the organelle as a series of invaginated membranous sheets, called cristae. ▯ The cristae contain a large amount of membrane surface which house the machinery needed for aerobic respiration and ATP formation ▯ Cristae increase the membranes surface area ▯ The membranes of the mitochondrion divide the organelle into two aqueous compartments one within the interior of the mitochondrion called the matrix and the second between the outer and inner membrane called the inter- membrane space ▯ The inner mitochondrial membrane is highly impermeable virtually all molecules and ions require special membrane transporters to gain entrance to the matrix ▯ In addition to enzymes the mitochondrial matrix also contains ribosomes, several molecules of DNA, which is circular and higher plants and animals. Thus mitochondria possess their own genetic material and the machinery to manufacture their own RNAs and protein ▯ Mitochondria extract energy organic materials and store it temporary in the form of electrical energy. More specifically the energy extracted from substrate is utilized to generate an ionic gradient across the inner mitochondrial membrane, a gradient across the membrane represents energy that can be tapped to perform work ▯ Oxidative phosphorylation: ▯ High energy electrons pass from co-enzymes (NADH FADH ) in 2he matrix to electron carriers (proteins)(respiratory enzyme complexes I, II, III, IV) in the inner mitochondrial matrix ▯ The electron carriers make up the electron transport chain ▯ The energy transfer at each complex is used to pump H from the matrix into intermembrane space ▯ The low energy electron is transferred to the terminal electron acceptor and H O 2 is produced ▯ Hydrogen is pulled back into the matrix through ATP synthase and ATP is produced ▯ Apoptosis or programmed cell death is a normal occurrence in which an orchestrated sequence of events leads to the death of a cell. Apoptosis is a neat, orderly process characterized by the overall shrinkage in volume of the cell and it’s  nucleus,  the  loss  of  adhesion  to  neighboring  cells,  the  formation  of  blebs  at   the cell surface, the dissection of chromatin into small fragments, and the rapid engulfment of the corpse by phagocytosis ▯ The intrinsic Pathway of Apoptosis is initiated by intracellular stimuli, proapoptotic proteins damage the mitochondria to leak proteins, cytochrome c (the released protein) commits the cell to apoptosis Chapter 8 and Lecture Notes ▯ Cisternae are stacks of flattened membrane-bound sacs ▯ The cytoplasm of the cell is divided into specialized membranous compartments for an analogous reasons ▯ Together the endoplasmic reticulum, Golgi complex, endosomes, lysosomes, and vacuoles form the endomembrane system in which the individual components function as part of a coordinated unit ▯ The organelles of the endomembrane system are part of the dynamic, integrated network in which materials are shuttled back and forth from one part of the cell to another. For the most part, materials are shuttled between organelles from the Golgi complex to the plasma membrane ▯ Transport vesicles are small membrane-bound vesicles that bud from a donor membrane compartment. They move through the cytoplasm and in a directed manner, often pulled by motor proteins that operate on tracks formed by microtubules and microfilaments of the cytoskeleton. When they reach their destination they fuse with the membrane of the acceptor compartment which receives  the  vesicle’s  soluble  cargo  as  well  as  it’s  membranous  wrapper ▯ Repeated cycles of budding and fusion shuttle a diverse array of materials along numerous pathways that traversed the cell ▯ A biosynthetic pathway can be discerned in which proteins are synthesized in the endoplasmic reticulum modified during passage Golgi complex and transported from the Golgi complex to various destinations. This route is also referred to as the secretar
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