1. Describe the pathway that proteins go through in order to get excreted.

They are synthesized on the ribosomes on the rough ER, which then enter the ER for modifications, after that, the proteins bud off and travel to the cis region of the golgi for further modification, then they bud off of the trans region of the golgi and are transported to the surface of the membrane where they may be excreted or put to use. 2. Describe the process of phagocytosis. Phagocytosis is when a phagocyte, such as a macrophge or microphage, engulfs dying red blood cells, bacterial cells, or food particles. The pseudopods surround the cell or particle completely, then it becomes a phagosome. Then the lysosomes move to the phagosome, and fuse with it, forming a phagolysosome, or secondary lysosome. The lysosomes contain digestive enzymes, which are only active under acidic pH, and so protons are pumped into the phagolysosome, which lowers the pH and activates the enzymes, and they then digest the cell or particle. 3. List all evidence supporting Lynn Marguliss Endosymbiotic Theory. a. Mitochondria and choloroplasts are same size as bacteria. b. Reproduce like bacteria. c. Have bacterial DNA. d. Have bacterial ribosomes which carry out bacterial protein synthesis e. Have lipid bilayer. f. Mitochondria have identical DNA to Rickettsia. 4. What are the components of the cytoskeleton, what is each one made out of, and what are their individual functions? MicrofilamentsMade up of actin. Function in cell movement (ameboid movement) and cell shape. MicrotubulesMade up of alpha-tubulen and beta-tubulen. Make up centrioles and spindle fibers during cell division, and pull chromosomes apart. Function in flagella and cilia for cell movement. Have 9+2 pattern. Uses motor protein dynein to power flagella which moves the microtubules past one another, and the nexin anchors the microtubules together, so when the dynein tries to slide the microtubules past each other, the nexin holds them together, causing the whole structure to bend. Look at figure 5.21 Also functions in moving vesicles. The motor protein Kinesin walks along the microtubule while holding a vesicle. This is for transport inside the cell. Intermediate filamentsmade up of fibrous proteins. anchor cell structures in place, such as the nucleus and other organelles. They also resist tension by reaching through the cytoplasm and connecting to the desmosomes. 5. What is the fluid mosaic model of membranes? The proteins are noncovalently embedded in the phospholipid bylayer by their hydrophobic regions, but their hydrophilic domains are exposed to the watery conditions on either side of the bilayer. These membrane proteins have a number of functions, including moving materials through the membrane and receiving chemical signals from the cells external environment. The carbohydrates associated with membranes are attached to either the lipids or protein molecules. Carbohydrates are located on the outside of the cell, where they may interact with substances out there. Carbohydrates are crucial in recognizing specific molecules, such as those on the surfaces of adjacent cells. the lipids in biological membranes are usually phospholipids, which are amphipathic. This allows for the hydrophobic tails to interact with the other tails, and the heads to interact with the watery environment. There are peripheral membrane proteins which do not penetrate the bilayer at all. Cholesterol molecules are interspersed among the phospholipid tails and influence the fluidity of fatty acids in the membrane. Some membrane proteins interact with the interior cytoskeleton. Some integral proteins cross the entire bilayer while others only penetrate partially. Carbohydrates are attached to the outer surface of proteins forming glycoproteins or they attach to lipids forming glycolipids 6. What is the difference between hypotonic, hypertonic, and isotonic? Cells in a hypotonic environment have a higher concentration of water on the outside than on the outside, and so the water moves into the cell, and eventually it causes the cell to lyse. Cells in a hypertonic environment have a lower concentration of water on the outside of them, so the water moves out of the cell, causing it to shrink. Cells in an isotonic environment have equal amounts of water on both sides of the membrane, and water diffuses evenly through the membrane. 7. What is the difference between active transport and passive transport? Active transport requires the input of energy to move a substance against its concentration gradient, by using the energy given off by passive transport or ATP. Passive transport does not require an input of energy and moves substances down the concentration gradient.

8. Describe Receptor-Mediated Endocytosis. Receptor-mediate endocytosis is specific for a substance. There is a receptor on the cell surface that can bind to a specific molecule, and once that molecule binds to it, the cellular membrane caves inward, taking in the substance that caused the receptor to activate. 9. What are the laws of thermodynamics? 1st law-Energy cannot be created or destroyed. 2nd law-Entropy always increases, and no reaction is ever 100% efficient. 3rd law-you can never cool anything to absolute zero. 10. What is activation energy and Gibbs-free energy? Activation energy is the energy that must be overcome in order for a reaction to proceed. Enzymes act as catalysts, which lower the activation energy of reactions, allowing the reactions to happen at a much faster rate. Gibbs free energy is the amount of energy gained or lost during an endergonic or exergonic reaction. 11. What are cofactors, coenzymes, and prosthetic groups. Cofactors are inorganic materials that must bind to an enzyme for it to function by altering its shape. These are usually ions, examples would be Zinc, copper, or iron. Coenzymes are organic materials that enzymes need to function. They can position the substrate and enzyme, or they may alter the shape of the enzyme so the substrate fits in the active site. An example would be NAD, FAD, or ATP. Prosthetic groups are also necessary for some enzymes to function. They attach to the enzyme, but are not always involved in the reaction. They may shape the enzyme, they may link the substrate to the enzyme, or they may assist in the reaction. 12. Describe competitive, noncompetitive, and irreversible inhibition. Competitive inhibition is when the competitor looks like the substrate and competes with the substrate for the active site. If the inhibitor occupies the active site, the substrate cannot, and the reaction rate slows down. Noncompetitive inhibition, or allosteric inhibition occurs when the inhibitor binds to an allosteric site on the enzyme, away from the active site. This causes a shape change in the enzyme, and it can no longer function. Adding more enzymes can increase the reaction progress. Both competitive inhibition and noncompetitive inhibition are reversible. Irreversible inhibition is when the inhibitor permanently binds to the enzyme and covalently bonds to the active site, which does not allow the substrate to access it. 13. What is feedback inhibition? Feedback inhibition is when the product of a reaction acts as the inhibitor. If lots of product is produced, then that competes with the substrate for the active side, thus slowing down the reaction until the produce is used up for its purpose. Once the product concentrations get low again, the substrate binds to the enzyme more frequently, and the product builds up once again. This is a method of regulating enzyme activity. 14. What is the difference between aerobic respiration, anaerobic respiration, and fermentation? Aerobic respiration takes place in the presence of oxygen. After glycolysis, the two pyruvate molecules enter the Krebs Cycle, producing ATP, CO2, NADH, and FADH2. The NADH and FADH2 are then used in the Electron Transport Chain (ETC), using Oxygen as the terminal electron acceptor. Produces about 32 ATP total. Anaerobic respiration is similar to aerobic respiration, however, at the end of the ETC, the terminal electron acceptor is NOT oxygen, it may be NO3, NO2, etc. Fermentation takes place when there is no terminal electron acceptor at all, and the pyruvate cannot undergo further oxidation after glycolysis. Therefore, pyruvate gets reduced to ethanol or lactic acid and NADH gets oxidized to NAD+ so that the NAD+ can be regenerated and used again in glycolysis for the net production of 2 ATP. 15. Explain how the electron transport chain functions in ATP production. The electrons carried by NADH and FADH2 from the citric acid cycle feed the electron carriers of the inner mitochondrial membrane, which pump protons out of the matrix into the intermembrane space. (NADH has more energy than FADH2, so it starts earlier in the ETC). The electrons pick up proton before entering the ETC. The proton pumping creates an imbalance of H+, causing both a concentration gradient, as well as an electrochemical gradient, and this imbalance is called the proton-motive force. The proton motive force drives protons back to the matrix through the enzyme ATP Synthase, causing the enzyme to spin and phosphorylate ADP to ATP. 16. What is a coupled reaction? A coupled reaction refers to two reactions simultaneously taking place and affecting the other one. An example would be in glycolysis, coupled reactions take place when the high-energy ATP gets hydrolyzed, forming ADP, and the energy given off is used to phosphorylate glucose. The energy given off by the first reaction was used to fuel the second reaction, thus a coupled reaction.