Biology 1450 Exam 2 Study Guide Fall 2024 PDF

Biology 1450 Biology I Fall 2024 Exam 2 study guide. Posted Friday, October 11 Exam 2 will cover chapters 5-8 of the text, and possibly part of chapter 9, which you should have read as they were addressed in lecture. P...

Biology 1450 Biology I Fall 2024 Exam 2 study guide. Posted Friday, October 11 Exam 2 will cover chapters 5-8 of the text, and possibly part of chapter 9, which you should have read as they were addressed in lecture. Part of chapter 5 was addressed on the first exam. Exam 2 will be worth 75 points, with about 60 points as multiple choice (2 points each), and the remaining points as diagrams or short answer. Chapter 5 (continued) Proteins When amino acids are linked together, they form a polypeptide. There are 20 amino acids commonly used for building polypeptides. What do these amino acids have in common? What is different about them, and how do these differences contribute to the physical and chemical properties of the resulting protein? The differences between primary, secondary, tertiary, and quaternary levels of structure were discussed in lecture and are presented in the book – know the differences between these. Also, where does the information for putting a particular polypeptide together come from? The idea of co-linearity was introduced (the correlation between directionality of a polypeptide and the directionality of gene information content); how is this idea significant relative to the “central dogma?” Nucleic Acids Nucleic acids are built up of nucleotide monomers, and each monomer is a composite of a phosphate, a ribose sugar (or its derivative, as deoxyribose), and a nitrogenous base. You should be able to sketch the orientation of these pieces relative to each other, and show how a polynucleotide is assembled (cartoon- style, as I have done in lecture). Be familiar with the conventions for drawing oligo- and polynucleotides: know which is the growing end of the chain, which is the 5’ and which is the 3’ end. Be able to compose a complementary antiparallel strand to a given template. Know the differences in the nucleotide compositions of RNA and DNA. Finally, recognize that any of these molecules may be modified, and sometimes they may be joined together to make a composite molecule, as in the case of a glycoprotein, which is a protein to which sugar monomers or polymers have been added. What is the significance? In this instance, you would recognize that in the manufacture of proteins, as sugars are not encoded in the same way as amino acids, the sugars must therefore be added by a separate modifying function apart from protein synthesis by the ribosome. Chapter 6 Chapter 6 presents the overall architecture of the eukaryotic cell. All cells, prokaryotic or eukaryotic, are bounded by a cell membrane or plasma membrane that encloses the cytoplasm. In addition, eukaryotic cells have several membrane-bound spaces within the cell. The nucleus is the central landmark of the eukaryotic cell, and it is the innermost starting point for the endomembrane system, most of which also makes up the “secretory system” due to its role in the secretion of proteins and polysaccharides from the cell. Know the features of the nucleus, and its membrane system, and show how it is connected to the next portion of the endomembrane system, the endoplasmic reticulum. You should be able to draw a flow diagram the follows the progress of protein synthesis from sites on the rough ER (why rough?) through the lumen to vesicles, the Golgi, and subsequent destinations outside the cell or in the lumens of other endomembrane system organelles. 1  While mitochondria and chloroplasts have membranes also, they are not part of the endomembrane system. Each of these shows evidence of an endosymbiotic origin, during which a prokaryotic organism was engulfed by a eukaryotic cell. Each has its specific functions in the cell. You should be able to diagram the anatomy of either of these correctly, showing the right number of membranes, naming the important membranes and spaces, and locating the genetic material within each. Additional features of cells that we examined were cytoskeletal elements (three kinds, with similarities and differences), cell walls, the extracellular matrix, and intercellular connections. We examined the semiautonomous organelles (the mitochondrion and chloroplast) noting the features they share with prokaryotic organisms, and that point towards their origins as endosymbiotic events. We also introduced other cell features such as the cytoskeleton, cell walls, and types of intercellular connections. Chapter 7 addressed functions associated with membranes, including transport processes. Many functions are performed by proteins associated with the membrane – you may be asked to demonstrate the different ways that proteins can be associated with membranes, and what these different kinds of associations imply about the protein’s structure. You should be familiar with the distinction between passive and active transport processes, and the kinds of membrane proteins that mediate these transport processes: Channels facilitate the selective diffusion of solutes down a potential gradient. They are like pores that allow only specific solutes to pass through. Channels may be “gated”, meaning that they may be opened or closed to permit or restrict solute movement. Carriers bind to specific solutes and deliver them across the membrane, most often down the potential gradient. Pumps are employed to drive solute transport against a potential gradient. The energy for this active transport must come from some other source, such as ATP or other solutes. The potential is “invested” in the solute that is moved against its potential. Specific examples that we saw were the proton-pump that used ATP, and cotransport (both symport and antiport mechanisms). Bulk transport processes deliver or capture material in vesicles. This is the means by which exocytosis and endocytosis occur. Finally, the selective permeability of the membrane can impact how water moves into and out of the cell in different environments. In a hypotonic environment (with a low solute concentration relative to the inside of the cell), water will enter the cell spontaneously, while in a hypertonic solution, water will be drawn out from the cell; under isotonic conditions, there is no net water movement across the membrane. Chapter 8 introduced the general concepts of metabolism, the changes in chemical structures and their energy content. We made a general distinction between catabolic and anabolic processes, the building or breaking down of biological molecules. Inextricably linked to these processes are the energies derived from or required for these reactions. Energy, the capacity to do work, can be seen in different forms (kinetic vs. potential), and the potential stored in biological molecules and solutes may be in the form of relative concentrations or it may be stored in the structure of the molecule itself, (for example, if it can be oxidized). The behavior of energy is described by the laws of thermodynamics: The first law states that energy is neither created nor destroyed (it can, however, change its form). The second law states that, with time, 2 the entropy of a system (the amount of disorder and non-useful energy) increases. Consequently, for a reaction to occur spontaneously, it must be accompanied by a decrease in “free energy” and an increase in the energy that is no longer freely available to do work. When a reaction has proceeded to the point at which there is no further change in free energy, then the system is said to have reached equilibrium. Metabolic reactions may release free energy (exergonic reactions) or consume free energy (endergonic reactions). Energy may be captured and exchanged between separate reactions in the form of energy- carrying molecules. ATP is an example of a molecule that is invested with energy at one site in the cell, and used as an energy source at other sites. In lecture and in your book we saw different examples of how ATP makes things happen – by forcing changes in the conformations of biological molecules, or by altering the reactivity of chemical intermediates in a reaction. We used a “reaction progress” graph to illustrate how the energy states of a system change as reactants react to become products, noting that there is an intermediate higher energy state – the transition state – that is unstable, and that requires that input of energy (activation energy) for the reaction to occur. Further we noted that enzymes function to increase the rate at which a reaction occurs by binding the reactants (substrates) and lowering the amount of activation energy needed for the reaction to progress. Finally we noted that enzymes allow the cell to control the rate of biochemical reactions, because the enzymes themselves are subject to control by different mechanisms. Total enzyme function can be increased or decreased by increasing the amount of enzyme protein in the cell, or by altering the enzyme function, by activation or inhibition, through interactions with other molecules such as proteins or metabolites. Sometimes the product of a biosynthetic path acts through “feedback inhibition,” inhibiting the enzymes of its own synthetic pathway once it has reached high enough levels. Chapter 9 described respiration, the release of energy from chemical structures, driven by stepwise oxidations, with the generation of energy-carrying ATP. Under aerobic conditions, the three major processes that contribute to respiration are glycolysis, the citric acid cycle, and the mitochondrial electron transport chain. Glycolysis = oxidation of sugars to organic acids Glycolysis occurs in the cytoplasm, and it splits a 6-carbon sugar glucose into two smaller fragments and oxidizes them to an organic acid, pyruvate. From each glucose, two ATPs are gained, and some high- potential electrons are captured in the form of NADH (these will be “cashed in” at the electron transport chain if oxygen is available). Citric acid cycle = complete oxidation of acids to CO2 The organic acids derived from glycolysis are completely oxidized to CO 2 during the citric acid cycle (also called the tricarboxylic acid cycle or the Krebs cycle). Decarboxylations and oxidations of organic acids drive the recovery of electrons as NADH and FADH2 to be delivered to the electron transport chain, and a small amount of ATP is also generated in the process. Electron transport chain = energy from electrons used to make ATP; this requires oxygen The electrons recovered from glycolysis and the citric acid cycles as NADH and FADH 2 retain high levels of potential energy. This energy is used to move protons against their potential gradient across the mitochondrial inner membrane, thus investing them with potential energy. When the electrons are depleted of energy, they are released to oxygen (O2) to make water. The potential of the protons is then discharged to generate large amounts of ATP. 3