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Biology- Organisms Exam 1 Textbook Notes

by: Lauren Maddox

Biology- Organisms Exam 1 Textbook Notes bio 114

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Lauren Maddox

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Summaries from the textbook for Bio 114
Biology of Organisms (Bio 114)
Dr. Oliver Hyman
Study Guide
Biology; Science; Organisms; Bio 114
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This 11 page Study Guide was uploaded by Lauren Maddox on Saturday March 12, 2016. The Study Guide belongs to bio 114 at James Madison University taught by Dr. Oliver Hyman in Spring 2016. Since its upload, it has received 67 views. For similar materials see Biology of Organisms (Bio 114) in Biology at James Madison University.


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Date Created: 03/12/16
CHEMICAL EVOLUTION • Chemical Evolution theory maintains that inputs of energy led to the formation of increasingly complex carbon-containing substances, culminating in a compound that could replicate itself. • At that point is when it switched from chemical evolution to biological evolution • A descendant of the original molecule became metabolically active and acquired a membrane. • The two different model systems that attempt to explain the process component of the theory of evolution: prebiotic soup model and surface metabolism model • Prebiotic soup model-proposes that certain molecules were synthesized from gases in the atmosphere or arrived via meteorites. Afterward they would have condensed with rain and went into the oceans. “Organic soup” allowed for the construction of larger, even more complex molecules • Surface metabolism model-dissolved gases came in contact with minerals lining the walls of deep-sea vents to form more complex organisms. • Stanley Miller studied the prebiotic soup model. He wanted to know if it was possible to re-create the first steps in chemical evolution by stimulating early-Earth conditions in lab. • He had a large flask that represented the atmosphere and contained methane, ammonia, and hydrogen. • This large flask was connected to smaller flask by glass tubing (ocean). To connect these two, he had the boiling water constantly. This added water vapor to the large flask. • As the vapor cooled and condensed, it flowed back into the smaller flask, and boiled again, the vapor was circulating constantly. This was important: if the molecules in the stimulated atmosphere reacted with one another, the rain would carry them into the ocean, and boom there is a prebiotic soup. • Miller also had electrotrodes going through them to stimulate lightning, which added pulses of intense electrical energy. • In samples of the mini ocean, he found large amounts of hydrogen cyanide and formaldehyde, and amino acids. • This claim was accepted, but soon refuted by researchers who said that early atmosphere was dominated by CO2, CO, and H2. • The sunlight that strikes Earth is made up of packets of light energy called photons • The ozone layer protects the earth from these high-energy photons in sunlight. • Researchers believe that when chemical evolution was occurring, large quantities of high-energy photons bombarded the planet. • Energy from photons can break up molecules by knocking apart shared elections- these fragments are called free radicals- have unpaired electrons in their outermost shells and are reactive. • A problem with the prebiotic soup model is that precursor molecules would have been diluted when they enter early oceans. Without the concentration, formalydehe and HCN would be unlikely to meet and react to form more complex molecules. • The surface metabolism model offers a solution- reactants are recruited in a defined space- a layer of reactive minerals deposited on the walls of deep-sea vent chimneys. Dissolved gases would be attracted by the minerals and concentrated on vent-wall surfaces. This would be critical to the rate at which the reaction products are formed. • A catalyst provides the appropriate chemical environment for reactants to interact with one another effectively. • Acetic acid is a big deal because 1. It can be formed under conditions that stimulate a hydrothermal vent environment, and 2. It is a key intermediate in an pathway that produces acetyl CoA, which is used by cells throughout the tree of life. • Vent minerals probably served as catalysts in the synthesis of acetic acid. • Organic molecules are molecules that contain carbon-bonded to other elements. • Carbon is the most versatile atom on Earth. • Carbon-carbon bonds represented a crucial step toward the production of the types of molecules found in living organisms. • Functional groups- the critically important H-, N, O, P and S containing groups found in organic compounds. • Haldane’s scientific theory- o Chemical evolution began with the production of small organic compounds from H2, N2, NH3 and CO2 o These small simple organic compounds reacted to form mid-sized molecules—amino acids, nucleotides, and sugars o Mid-sized molecules formed to build proteins, nucleic acids, and carbohydrates o Life became possible when one of these large, complex molecules acquired the ability to replicate itself. • Researchers believe that amino acids were the first replicating molecule meaning are proteins the first replicating molecule? To answer this, information, replication, and evolution. • Amino acids have a central c atom, h atom, amino functional group (NH2), and carboxyl functional group (COOH), and a distinctive r group. • Charges on functional groups are important because they help amino acids stay in solution, and they affect the chemical reactivity. • Monomer-amino acid, nucleotide, sugar • When monomers form together-polymer. The process of linking them together is called polymerization • Polymerization decreases the disorder, or entropy of the molecules involved. • Monomers polymerize through condensation reactions, also known as dehydration reactions—newly formed bonds results in the loss of water molecule. • Hydrolysis- breaks polymers apart by adding a water molecule. This dominates because it increases entropy and is favorable energetically. • Polymerization would only occur if there is a high concentration of amino acids to push the reaction toward condensation. • In hot environments- amino acid formation and polymerization. Also in cool water if carbon or sulfur containing gas is present • The overall shape of a single polypeptide is called a tertiary structure. Level Description Stabilized Primary The sequence of amino Peptide bonds acids in a polypeptide Secondary Formation of a helices Hydrogen bonding and b pleated sheets in a between groups along polypeptide the peptide-bonded backbone, depends on primary structure Tertiary 3d shape of polypeptide Bonds and other interactions between r- groups and the peptide bonded backbone- primary structure Quaternary Shape produced by Bonds and other combinations of interactions between r- polypeptides groups and the peptide bonded backbone- primary structure • Proteins can be catalysis- speed up chemical reactions. Proteins that function as catalyst are enzymes • Proteins called antibodies complement proteins attack • Motor proteins and contractile proteins are responsible for mobility • Proteins are involved in carrying and receiving signals from cell to cell inside the body • Structural proteins make up body components like fingernails and hair • Proteins allow particular molecules to enter and exit cells or carry them through the body • Enzymes are effective catalysts because they bring reactant molecules together-substrates, so the atoms involved can interact. • Fischer’s lock and key- enzymes are locks and keys are substrates. • The location where substrates bind and react is the active site- where catalysis actually occurs. • Nucleic Acids • Made up of a five-carbon sugar, a nitrogenous base, and a phosphate group (nucleotides). • Two types of nucleic acids are dna and rna • The nitrogenous bases are purines (A and G) and the pyrimidine’s (C U and T) • Rna uses U and dna uses T • Polymerization reactions that join nucleotides into nucleic acids are catalyzed by enzymes, which need an input of energy (not spontaneous). • An activated nucleotide is ATP. • The addition of one or more phosphate groups raises the potential energy of substrate molecules enough to make an otherwise nonspontaneous reaction possible. • DNA and RNA have a sugar-phosphate backbone, created by phosphodiester linkages, and a sequence of any or 4 nitrogenous bases that extend from it. • They both have secondary structures as well, and they are formed by hydrogen bonding between the nitrogenous bases. • DNA carries the information for growth and production • DNA can self-replicate, but it can’t catalyze the reactions to self- replicate. • RNA can catalyze because it has so many different structures, DNA cannot because the structures are so simple. • Proteins have the most complex structure, then RNA, then DNA. • RNA contains information and can self-replicate. It can also catalyze reactions • Catalytic RNAs or ribozymes. • To make a copy of itself, the first living molecule had to o Provide a template o Catalyze polymerization reactions that would link monomers into a copy of the template • Sugars • Carbohydrates, or sugars, have monomers called monosaccharide’s and polysaccharides. • Sugars provide chemical energy in cells and make molecular building blocks that are needed for larger compounds • The synthesis of sugarscouldd have been catalyzed by minerals found in the walls of deep-sea hydrothermal vents • Polysaccharides played little to no role in the origin of life because – no mechanism for polymerization of monosaccharide’s, no polysaccharide has been discovered that can catalyze polymerization reactions, the monomers in polysaccharides are not capable of complementary base pairing—they can’t be templates. • Lipids, Membranes and the First Cells • The cell membrane, aka plasma membrane, separates life from nonlife. • It is a selective barrier, keeps damaging compounds out, reactants collide more frequently, chemical reactions necessary are more efficient • Lipid- carbon containing compounds found in organisms, nonpolar and hydrophobic • Fatty acids and isoprene’s are key building blocks of lipids (have carbon bonds) • Hydrocarbon chains that have only single bonds between carbons are saturated • If one or more double bonds exist in the chains they are unsaturated. • Saturated-solid • Unsaturated-liquid • Lipids are characterized by their physical property—insolubility in water • Phospholipids consist of glycerol that is linked to a phosphate group and two hydrocarbon chains. The phosphate group is bonded to a small organic molecule that is charged or polar. • They stored chemical energy, act as pigments that capture or respond to sunlight, serve as signals between cells, form waterproof coatings on leaves and skin, act as vitamins in cellular processes • Membrane-forming lipids have a polar hydrophilic region, and a nonpolar hydrophobic region • The head region has polar covalent bonds and interacts with water • The hydrocarbon tails are nonpolar and hydrophobic • Amphipathic- contain both hydrophilic and hydrophobic elements • Instead of dissolving in water, these structures either assume these structures- micelles or lipid bilayer • Micelles are tiny droplets created when the hydrophilic heads of a set of lipids face the water and form hydrogen bonds, while the hydrophobic tails interact with each other in the interior • Lipid bilayer- created when two sheets of lipid molecules align. The hydrophilic heads in each layer face the surrounding solution, while the hydrophobic tails face one another inside the bilayer • These two structures form spontaneously • Liposomes are the artificial membrane-bound vesicles • Small, nonpolar molecules move across the bilayers quickly, while large molecules and charged are slow or don’t at all. Ions cant at all. Small polar molecules can • Saturated and long hydrocarbon are very strong. Unsaturated and short are easy to pass through. • As temp drops, the harder it is to pass • Movement of molecules and ions that results from their kinetic energy is known as diffusion • A difference in solute concentrations is called a concentration gradient • When there is a concentration gradient, they move from high to low— spontaneous • Diffusion of water is osmosis. Only unbound water molecules can cross. —Low to high (high water to low water) • If there is a higher concentration of solute outside of the membrane, water is going there, so the cell shrinks (hypotonic to the outside) • If there is a higher concentration of solute inside the membrane, water goes inside, so the membrane swells or burst (hypertonic to the outside) • If the concentration is the same, water can move in and out freely and there isn’t a change. (Isotonic) • RNA probably became surrounded by a lipid bilayer • Proteins that are amphipathic can be inserted into the lipid bilayer and affect its permeability. • Ions can cross membranes through ion channels- form pores in a membrane, high to low concentration, like charge to unlike charge • Ions move in response to a combined concentration and electrical gradient- electrochemical gradient • Cystic fibrosis- people have large amounts of mucus. Caused by defect in a membrane protein that allow chloride ions to move across plasma membranes—reduced chloride transport. Water would be stuck to chloride ions (bound water molecules) so they couldn’t maintain mucus development • Channel proteins are selective—has a structure that only permits a particular type of ion or small molecule to pass through it. • Aquaporin’s-allow water to pass through membranes really fast. • Gated channels (like aquaporin’s and ion channels) open or close in response to a signal, like the binding of a particular molecule or a change in electrical voltage. • Passive transport is powered by diffusion along an electrochemical gradient • Facilitated diffusion- the passive transport of substances that otherwise would not cross a membrane readily. • Carrier proteins, also facilitate diffusion are specialized membrane proteins that change shape during the transport process • Active transport is going against the gradient—requires energy • ATP provides energy for active transport by transferring the phosphate group to an active transport protein called a pump • Evolution of membrane proteins- internal environment that contained the substances required for manufacturing atp and copying ribozymes • Free energy is describing the amount of energy that is available to do work • Energy cannot be created nor destroyed, but only transferred and transformed- first law of thermodynamics • When reactions are spontaneous, they are said to be exergonic. When they aren’t- endergonic • When an atom or molecule lose one or more electrons-oxidized • When an atom or molecule gains electrons-reduced • Oxidation is the exergonic half-reaction and the reduction is the endergonic half reaction • Reduction often adds H’s, oxidization often looses them • When ATP reacts, it is exergonic, forms ADP and P-inorganic phosphate • ATP hydrolysis is exergonic because the entropy of the products is higher than that of the reactants; ATP breaks down into ADP and P. • Glucose is the most common source of chemical energy • A cell contains only enough ATP to last from 30 seconds to a few minutes. It is unstable and isn’t stored. • Organisms use the energy in sunlight to reduce CO2 to glucose and carbohydrates. Photosynthetic species use the glucose that they produce to make ATP • Starch and glycogen are like saving accounts for chemical energy, ATP is like cash. Storage carbohydrates are first hydrolyzed into their glucose monomers. The glucose is then used to produce ATP through cry or fermentation. • When glucose is oxidized- heat is released. • Respiration results in the complete oxidation of glucose into co2 and water. Fermentation doesn’t fully oxidize glucose. Small-reduced organic molecules are produces as waste. CR releases more energy • CELLULAR RESPIRATION 1. Glycolysis- one 6-carbon molecule of glucose is broken down into two molecules of pyruvate. Atp is produced from adp, and nad+ is reduced to form nadh 2. Pyruvate processing- processed to release one molecule of co2 and the rest is used to form acetyl CoA. Nad+ is reduced to NADH 3. Citric acid cycle- acetyl is oxidized to two molecules of co2, ATP and NADH is produced. Fad to fadh2 4. Electron transport- electrons from NADH and fadh2 go to the electron transport chain. The energy released is used to create a proton gradient across a membrane to make ATP. This mode of atp production links the phosphorylation of adp with the oxidation of nadh and fadh2- called oxidative phosphorylation • Sets of reactions that break down molecules are called catabolic pathways • Sets of reactions that synthesize larger molecules from smaller components are anabolic reaction—use atp • In cells, enzymes break down fats to release the glycerol and convert the fatty acids into acetyl CoA molecules. Glycerol and be processed and go to glycolysis, and CoA goes to the critic acid cycle. • In glycolysis everything but glucose and pyruvate are phosphorylated. • Mitochondria has two membranes- inner and outer, the interior is filled with cristae. Short tubes connect the cristae to the main part of the inner membrane. The region inside the inner membrane but outside the cristae is the mitochondrial matrix. • Pyruvate moves across the mitochondrion’s outer membrane through small pores. • Inside, pyruvate reacts with a compound called CoA, to produce acetyl CoA. • As it is being processed, one of the carbons is oxided to co2, and nad+ is reduced to NADH. The remaining two CoA, is transferred CoA. • When ATP is abundant-coa and NADH are in high concentration- pyruvate processing shuts down. • These reactions occur in the mitochondrial matrix. • In the critic acid cycle- the energy released by acoa is used to produce three NADH and one of fadh2. Also ATP is produced. • It has to run twice for each glucose molecule • The atp molecules created in glucose oxidation are produced by substrate-level phosphorylation and can be used to drive endergonic reactions • The co2 molecules are disposed of as a waste • The molecules responsible for the oxidation of NADH and fadh2 are designated the electron transport chain. As electrons are passed from one molecule to another in the chain, the energy released by the redox reactions is used to move protons across the inner membrane of mitochondria. • The etc. transports protons from the matrix, across the inner membrane, and into the intermembrane space. • Chemiosmosis- use of proton gradient to drive energy-requiring processes, like ATP. • A proton gradient can be used to synthesize ATP via ATP synthase. • Atp production depended solely on the existence of a proton-motive force, which based on a proton electrochemical gradient. • Atp synthase is a motor-flow of protons make the rotor and shaft to spin. As it spins, ADP goes to ATP. • Species that depend on oxygen as an electron acceptor use aerobic respiration. • Where oxygen isn’t high, organisms can use sulfate and nitrate as acceptors, and h2 or h2s, or ch4 as electron donors. This is anaerobic respiration. • Anaerobic makes less ATP. • Fermentation is a metabolic pathway that regenerates nad+ by oxidizing stockpiles of NADH. The electrons are then transferred to pyruvate. It allows glycolysis to continue producing ATP. Test Two • Photosynthesis is an endergonic suite of redox reactions that produce sugars from carbon dioxide and light energy. • Cellular respiration is an exergonic suite of redox reactions that produces co2 and atp from sugars • Two distinct reactions in photosynthesis—one that uses light to produce o2 from h2o and one that converts co2 into sugars. • The reactions that reduce co2 to sugars is called the Calvin cycle • One set of the reactions is triggered by light, the other is the Calvin cycle and that requires the products of the light reactions • In the light reactions, the electrons go from nad+, to nap+, and then NADPH. Some of the energy released is used to produce ATP. • In the Calvin cycle, the electrons in NADPH and the potential energy in ATP are used. The resulting sugars are used for cellular respiration. • Photosynthesis is in chloroplasts. • Pigments absorb wavelengths; we see the colors that they don’t absorb. The most abundant pigment in the thylakoid membrane is chlorophyll. • Photosynthesis converts electromagnetic energy in the form of sunlight into chemical energy in carbon or carbon hydrogen bonds of sugar. • When a photon hits a chlorophyll molecule, the photon’s energy is transferred to an electron in the chlorophyll molecule. This electron is said to be excited or raised to a higher energy state. • If the excited electron falls down to ground state, the absorbed energy is released as heat and light. • Chlorophyll molecules and accessory pigments are organized by an array of proteins to form the antenna complex and the reaction center. These complexes, along with the molecules that capture and process excited electrons form a photosystem • Red or blue photon strikes pigment in antenna complex-energy is absorbed and an electron is excited. This energy is passed to a chlorophyll molecule, where another electron is excited. This is known as the resonance energy transfer. • This only happens between pigments of different wavelengths photons (absorbing higher energy photons to absorbing lower energy photons). • The potential energy drops at each step • Once the energy is transferred, the original excited electron is dropped back to original ground state—the energy is directed towards the reaction center. • When a chlorophyll molecule is excited in the reaction center, its excited electron is transferred to an electron acceptor. When the acceptor becomes reduced, the energy transformation event that started with the absorption of light becomes permanent. • Electromagnetic energy is transformed to chemical energy. • Without light- electron acceptor doesn’t accept electrons, remains oxidized, its endergonic • With light- it is reduced and is exergonic. • For photosystem II- the redox reactions that occur in both etcs results in protons being actively transported from one side of a membrane to another. The resulting proton electrochemical gradient forms a proton-motive force that drives ATP production via ATP synthase. • Photosystem II triggers chemiosmosis and atp synthesis in the chloroplasts • Photosystem I has two electrons that are excited in the reaction center, then the reaction center pigments are oxidized, and the high energy electrons are passed through a series of carriers inside the photosystem, then a molecule called ferredoxin and then to the enzyme called nadp+ reductase. This transfers two electrons and a proton to nadp+. This forms nadph • Electrons from photosystem I are used to produce NADPH • Electrons from photosystem II are used to produce a proton-motive force that drives the synthesis of ATP • In combination, they both produce chemical energy stored in ATP and NADPH. • They are connected by the electron transport chain • O2 comes from enzymes that evolved that could catalyze the oxidation of water. • Created the ozone layer • Carbon fixation is the addition of co2 to an organic compound. It is a redox reaction, it is reduced. • THE CALVIN CYCLE 1. Fixation phase- the Calvin cycle begins when co2 reacts with RuBP. This phase fixes carbon and produces two molecules of 3PGA. 2. Reduction phase- 3PGA is phosphorylated by ATP and then reduced by electrons from NADPH. This forms G3P. 3. Regeneration phase- the rest of g3p keeps the cycle going by serving as substrate for the 3 phase in the cycle: reactions that use additional ATP in the regeneration of RuBP. • All take place in the stroma. • Clarified how the ATP and NADPH produced by light-capturing reactions allows cells to reduce co2 gas to carbohydrate. • The products of the Calvin cycle can enter several pathways • The most important of these reactions is called gluconeogenesis- produces glucose and fructose from g3p. This glucose is combined with fructose to form sucrose. • If sucrose is delivered to rapidly growing parts of the plant, it is broken down to fuel cell respiration and growth. • When photosynthesis is proceeding rapidly and there is an abundant amount of sucrose, the glucose is polymerized to form starch. It acts as a temporary sugar storage product. • At night the starch in the leaves is broken down to make sucrose molecules, and the sucrose is broken down via cell respiration or transported to other parts of the plant.


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