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U-M CHEM 451 - Exam 1 Study Guide

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Chem 451 1st EditionExam # 1 Study Guide Lecture 2-3 (January 9 & January 12)Origin of Life Till TodayExplain the significance of the Miller-Urey discharge experiment.The two scientists from U. Chicago took molecules that they believed represented the major components of the Earth’s atmosphere at the origin of life and refluxed them in a closed container. The gases were methane, ammonia, hydrogen cyanide, carbon dioxide, and nitrogen gas. They exposed the system to electrical discharge to simulate lightning storms. About a month later, they opened the flask and analyzed the contents via chromatography. Instead of the simple inorganic molecules that were originally placed in the system, the scientists observedthat much of the contents were organic compounds. Additionally, many amino acids were foundin the mixture. This experiment showed that organic compounds could be easily condensed under conditions similar to those present on the early earth.What is a heterocycle?In 1961, Juan Oro of the University of Houston found that by condensing hydrogen cyanide and ammonia in an aqueous solution, the nitrogenous base adenine could be spontaneously produced in a six-step cycle known as a heterocycle. Adenine has great biological significance because it is a building block of DNA and RNA.What is a possible role of clay in the origin of life?Clay is good for absorbing organic molecules. It has been proposed that the surface of clay was used as a catalyst for amino acids to condense together to form proteins. It could also have aided in these condensation reactions via acid-base catalysis. Finally, clay pockets may have helped exclude water because they are not permissible to H2O.We know that hydrolytic decay technically decreases entropy. What are possible sources of energy that helped to drive this increase in complexity?- Pyrite (FeS2): the sulfur has a low oxidation state that can be oxidized to sulfate; redox reaction creates intrinsic energy- Thioesters: formed via condensation of carboxylic acids and pyrite, as well as thermal ventconditions (high temperature, acidic conditions); thioesters give rise to various forms of energy by a) ATP and PPi, b) catalysts for RNA, and c) reduction for organic acids and aldehydesWhat are the three requirements for Darwinian evolution to occur at both the molecular and organismal level?Replication, mutation, and selection.Explain Levinthal’s paradox and the theory of protein folding that it disproves.Assuming that a 100 amino acid protein has only two angles (φ and ψ around α-carbon) that can be changed between 3 different positions, there are an estimated N = 998 ≈ 3*1093 possible conformations. This means that even if it only takes one picosecond to try out each possible conformation, it would take an entire lifetime to form a functional protein if only random search were at work. This disproves the protein theory that nature works as a blind watchmaker and that protein formation is simply improbable and not inevitable and is driven by small energetically favorable downhill reactions.What are fractals?Fractals are complex geometric structures that emerge from a recursive mathematical formulae.They are universal in the natural landscape form, ie.) how a simple broccoli flower resembles a tree due to similar rules of growth. A tree is approximately self-similar, meaning that a small piece of the three looks like a smaller version of the entire tree. Briefly explain some of the test tube experiments done to regenerate early RNA that we covered in lecture.-RNA Replicase (2001, Bartel et al): enzyme that catalyzes the replication of RNA from an RNA template; contrasts from DNA-dependent RNA polymerase, which catalyzes transcription from RNA to DNA. This is significant because it does not require DNA to extent an RNA primer.-RNA Nucleotide Synthase (1998, Unrau & Bartel): enzyme that builds pRpp (precursor to nucleotide metabolism and amino acids) which fuses together with a nucleobase to form a nucleotide. This enzyme is also used to rebuild itself.-Moore and Steitz, 2000: presented a model of the ribosome via crystallography. They showed that the ribosome is made up mostly of RNA, giving rise to the theory of the ribozyme.How does Darwinian chemistry relate to early life metabolism?The self-replicating RNA replicase molecule creates a feedback loop. With energy and mistakes in replication that are helpful to other enzyme activities, mutation creates additional moieties. This leads to expansion of the hypercycle in metabolism.How did primitive cells in the primordial world distinguish between self and non-self?Cooperative activities in the hypercycle need to be separated from others that are not in the same hypercycle path in order for efficient evolution to take place. Primitive cells used hydrophilicity to distinguish self and non-self.- Hydrophobic ends point up in the air and hydrophilic ends point toward water- With energy, a spray droplet forms a lipid bilayer, encapsulating compounds of interest together in the middle- Self-organization allowed entities interacting in a hypercycle to separate from the environment.- The self-contained entity within the membrane can replicate, mutate, and undergo selection. Cellular evolution occurs.Lectures 4-7 (January 14, 16, 21, 23) Enzyme KineticsWhy are enzymes advantageous over chemical catalysts?- Higher reaction rates- Require milder reaction conditions – while chemical catalysts usually favor extreme conditions, such as high temperatures and acidic pH, enzymes work favorably at body temperature, in water, and near a neutral pH- Greater reaction specificity with high-fidelity (very little error)- Can be regulated (allosterically, covalently, end-product inhibition, and gene expression regulation)- Can evolve to be more efficient.What kinds of interactions give rise to the binding specificity of enzymes?- Hydrophilic/hydrophobic interactions- Van Der Waals- Dipole-dipole interactions- Hydrogen bonding- Ion-ion interactions (positive-negative)- Sterics – dimensionality in space- Water – surrounds the substrate in solution and hydrogen bonds with the substrate. Water molecules fill the enzyme pocket and must be displaced in order to bind with the enzyme. This costs energy.Explain structural dynamics using DHFR as an example. Dihydrofolate reductase catalyzes the reduction of dihydrofolate to tetrahydrofolate. NADPH transfers a hydride ion to one of the carbons in dihydrofolate, reducing the


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