Bios 208 1st EditionExam # 4 Study Guide I. Enzymes, structure and function, and coenzymesA. Enzymes are biological catalysts.B. Substrates bind to an enzyme’s active site.C. Upon binding, the shape of the enzyme and its active site change “induced fit”.D. The transition state occurs here; this is where old bonds are broken and new bonds are made.E. Free enzyme, free substrates.F. Substrates bind to the active site (“lock-in-key fit”).G. Bonds are strained, and then broken at the transition state, which requires E. EA is lowerwith an enzyme than without.H. New bonds form to make the products.I. Products are released.J. The enzyme is unchanged. Repeat steps 1-5 K. Temperature (top): human enzymes vs. heat-tolerantL. Bacteria pH (bottom): human stomach vs. intestinal enzymesM. Co-factors assist enzymesN. Inorganic co-factors: e.g., ions such as Fe in hemoglobinO. Co-enzymes are organic cofactors (i.e., they contain carbon; e.g., NADH)II. Allosteric inhibition of enzyme activityA. Allosteric regulators. An enzyme can have active and inactive forms.B. Activators hold the enzyme in an active form and increase enzyme activityC. Inhibitors hold the enzyme in an inactive form and decrease enzyme activityIII. Competitive inhibition of enzymes and Feedback RegulationA. Enzyme activity can be reduced by cellular inhibitors.B. Competitive inhibitors bind to the active site of an enzyme, which prevents the substratefrom bindingC. Non-competitive inhibitors bind to an allosteric site (i.e., not the active site). Structure ofactive site is changed, so substrate no longer can bind.D. Feedback inhibition of an enzymatic pathwayE. Isoleucine (Ile) biosynthesis: anabolic pathway with 5 enzymatic steps.F. Product of the first reaction is the substrate for the second reaction.G. Final product (Ile) is the allosteric inhibitor of the first enzyme (rxn.#1).H. High [Ile] low activityI. Low [Ile] high activity; “turn on “enzymes and make more IleIV. ATPA. ATP (adenosine triphosphate) is the cell’s energy shuttleB. ATP is composed of ribose (a sugar), adenine (a nitrogenous base), and three phosphate groupsC. ATP powers cellular work by coupling exergonic reactions to endergonic reactions •D. A cell does three main kinds of work a) Chemical b) Transport c) Mechanical E. To do work, cells manage energy resources by energy coupling, the use of an exergonic process to drive an endergonic one F. Most energy coupling in cells is mediated by ATPG. The bonds between the phosphate groups of ATP’s tail can be broken by hydrolysis H. Energy is released from ATP when the terminal phosphate bond is broken I. This release of energy comes from the chemical change to a state of lower free energy, not from the phosphate bonds themselvesJ. The three types of cellular work (mechanical, transport, and chemical) are powered by the hydrolysis of ATPK. In the cell, the energy from the exergonic reaction of ATP hydrolysis can be used to drive an endergonic reactionL. Overall, the coupled reactions are exergonicV. Early Light MicroscopyA. Understanding cell biology had to await the development of light microscopesB. Robert Hooke built one of the first microscopes and Wrote Micrographia (1665).C. He observed many structures with a simple microscope.D. Cork (from bark of an oak tree) contains “little rooms” or CELLS.E. Hooke also observed a flea in great detail.F. Robert Hooke Microscope (1635-1703)VI. Cell TheoryA. Cell Theory (1830’s -1850’s; Schwann, Schleiden, Virchow, others)B. All organisms are composed of one or more cellsC. The cell is the smallest, simplest unit of lifeD. All cells arose by division of pre-existing cellsE. Implications: Life evolved once. All organisms are descended from these cells.VII. Light microscopy and Electron microscopyA. Units (e.g., 1 m = 1000 mm = 106 μm = 109 nm)B. Cell dimensions (on each side):C. Prokaryotic cell: ~ 1-10 μmD. Eukaryotic cell: ~ 10-100 μmE. Resolution is the ability to discern fine detail. Approximate limits of practical resolution are:F. Human eye: 0.2 mmG. Light microscope: 0.2 μm (~1000x better than eye)H. Electron microscope: 2 nm (~100x better than LM)VIII. Animal cells and plant cellsA. Animal and plant cellsa) Nucleusb) Ribosomec) Plasma membraned) Endoplasmice) Reticulumf) Golgi apparatusg) MitochondrionB. Animals onlya) Lysosomeb) Flagellumc) CentrioleC. Plants onlya) Chloroplastb) Cell wallc) Central vacuoled) PlasmodesmataIX. Cell fractionationA. Homogenize: Cells are disrupted (e.g., with a blender)B. Centrifuge: Spin faster higher centrifugal force (g = force of gravity). At any given g-force, largest particles will be pelleted, and smaller particles will be in the supernatant.C. Differential centrifugation yields “fractions” enriched in various organelles or structuresD. P1 (1k x g): nuclei, cell debrisE. P20 (20k x g): mitochondria, chloroplasts, lysosomesF. P80 (80k x g): microsomal membranes (ER, Golgi Apparatus, Plasma Membrane, etc.)G. P150 (150k x g): ribosomesH. S150 (150k x g supernatant):cytosol; proteins, amino acids, ions, etc.X. Cell sizeA. Small cells have a high surface area to volume ratio (SA:Vol). This ratio must be optimal.B. Large organisms are made from many small cells, not a few large cells.C. This allows efficient transport of materials into and out of a cell if there is more membrane relative to cell volume. Goodies in; Garbage out “GiGo”D. Small volumes allow more efficient communication inside cell and allows the nucleus to direct events in the cell..e.g. protein synthesis.E. Animal Cells are 10-100 micrometers in sizeF. 1 micrometer = 1x10-6 mXI. Golgi, Smooth and RoughER, and LysosomesA. Golgi Apparatusa) Group of stacked cisternae; not interconnected.b) 2 sides:1. cis or forming face2. trans or maturing facea) Proteins from Rough ER are delivered in vesicles to the cis face; proteins go through each cisterna sequentially; proteins (and attached sugars) are modified sequentially.b) Assembly line modification of proteins. e.g. addition of sugar chains which act as “sorting codes” for delivery to different parts of cell, or secretion.c) Mature proteins are: 1. Sorted2. Packaged into vesicles 3. Delivered to other parts of the cell.B. Smooth Endoplasmic Reticuluma) Smooth ER (SER) Membrane tubules are interconnected with Rough ER, but no ribosomes are attached.b) Functions of Smooth ER in various cell typesc) Lipid synthesis. (most cells)d) Steroid synthesis. (adrenal glands, testes,