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Exam II - study guide

by: Megan Smith

Exam II - study guide Biol 1103k

Megan Smith
GPA 3.6

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these are all the notes from the book for exam two over chapters 6,7, and 8.
Introductory biology I
David blaustein
Study Guide
biology study guide
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This 16 page Study Guide was uploaded by Megan Smith on Sunday February 21, 2016. The Study Guide belongs to Biol 1103k at Georgia State University taught by David blaustein in Summer 2015. Since its upload, it has received 78 views. For similar materials see Introductory biology I in Biology at Georgia State University.


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Date Created: 02/21/16
Date CHAPTER 6 – ENERGY FLOW IN THE LIFE OF A CELL 1. WHAT IS ENERGY i. Energy • The capacity to do work ii. work • the transfer of energy to an object, causing the object to move iii. Chemical energy • Energy available in the bonds of molecules iv. There are two types of energy : a. potential energy i. Stored energy, includes the chemical energy available in biological molecules and other molecules b. kinetic energy i. the energy of movement • Under the right conditions, kinetic energy can be transformed into potential energy, and vice versa B. The laws of thermodynamics describe the basic properties of energy i. the law of thermodynamics • describes the quantity ( the total amount) and the quality ( the usefulness) of energy. ii. the first law of thermodynamics • States that energy can neither be cre ated nor destroyed by ordinary processes iii. (hypothetical) - Closed system • Energy can neither lea ve nor enter • the total amount of energy before and after any process will be unchanged iv. law of conservation of energy • often the name for the first law of thermodynamic v. Energy can be converted from one form to another vi. Second law of thermodynamic • When energy is converted from one form to another, the amount of useful energy decreases. • No energy conversion process is 100% efficient in using energy to achieve a specific outcome vii. Entropy • Tendency towards loss of complexity, orderliness, and useful energy • The concurrent increase in randomness, disorder, and less useful energy 2. HOW IS ENERGY TRANSFO RMED DURING CHEMICAL REACTIONS? i. Chemical reaction • A process that forms or breaks the chemical bonds that hold atoms together • Convert one set of chemical substances, the reactants, into another set, the products. ii. Exergonic • Energy out • The reaction releases energy; that is, if the starting reactants contai n more energy than the end products iii. Endergonic • Energy in • Requires a net input of energy; that is, if the products contain more en ergy than the reactants • Require a net influx of energy from an outside source B. Exergonic reactions release energy i. The total energy in the reactant molecules is much higher than in the product molecules C. Endergonic reactions require a new input of energy i. The reactants contain less energy than the products do D. All chemical reactions require activation energy to begin i. Activation energy • The energy “push” in a chemical reaction • Shells of negatively charged electrons surround all atom • Activation energy is the energy that is required to overcome the repulsive electrical forces between the electron shell so that they can move close enough together to react • Can be provided by the kinetic energy of moving molecules 2 3. HOW IS ENERGY TRANSP ROTED WITHIN A SHELL i. Energy carrier molecules • High-energy molecules that are synthesized at the site of an exergonic reaction, where they capture some of the released energy B. ATP and electron carriers transport energy within cells i. Adenosine triphosphate (ATP) • Many exergonic reactions in cells, such as breaking down sugars and fats , produce ATP • the most common energy carrier molecule in the body • a nucleotide composed of the nitrogen containing base , adenine, the sugar ribose, and three phosphate groups • sometimes call the “Energy currency” of cells • diffuses throughout the cell, carrying energy to sites where endergonic reactions occur • there is energy is liberated as it is broken down, regenerating ADP and Pi • not a long term energy -storage molecule ii. adenosine diphosphate (ADP) • inorganic phosphate • requires an input of energy, ATP synthesis is endergonic iii. electron carriers • captures energetic electrons, along with hydrogen ions • loaded electron carriers donate their high -energy electrons to other molecules which a re often involved in pathways that generate ATP C. Coupled reactions link exergonic with endergonic reactions i. Coupled reaction • An exergonic reaction provides the energy needed to drive an endergonic reaction using ATP or electron carriers as intermediaries • The energy released by exergonic reactions must always exceed the energy needed to drive the endergonic reaction • Energy is transferred from place to place by energy carrier molecules such as ATP 4. HOW DO ENZYMES PROMO STE BIOCHEMICAL REAC TONS i. Catalysts • Molecules that speed up the rate of reaction without themselve s being used up or permanently altered • All catalysts share three important properties 3 a. Speed up the r eactions by lowering the activation energy required for the reaction to begin b. Can speed up both exergonic and endergonic reaction, but they cannot make an endergonic reaction occur spontaneously c. Are not consumed or permanently changed by the reactions they promote B. Enzymes are biological catalysts i. Enzymes • Called employ highly specified biological catalysts called enzymes • Nearly all of which are proteins C. The structure of enzymes allows them to catalyze specific reactions i. The function of an enzyme is determined by its structure ii. Active site • Reactants molecules can enter this site iii. Substrates • Reactant molecules D. Enzymes, like all catalysts lower activation energy 5. HOW ARE NEZYMES REGULATE D i. Metabolism • The sum of all its chemical reactions ii. Metabolic pathway • Many chemical reactions, such as those that break down glucose into CO2 and water, are lined in sequences called metabolic pathways B. Cells regulate metabolic pathways by controlling enzyme synthesis and activity i. The rate of a reaction will depend on how many substrate molecules diffuse into the active sites of enzyme molecules in a given time period ii. Increasing the concentration of the substrate or enzyme (or both) will increase the reaction rate C. Genes that code the enzymes may be turned off or on D. Some enzymes are synthesized in inactive forms i. Some enzymes re synthesized in an inactive form that are activated under the conditions found where the enzyme is needed. E. Enzyme activity may be controlled by competitive or non competitive inhibition i. Competitive inhibition 4 • Substance that is not the enzyme’s normal substrate can also bind to the active site of the enzyme, competing with the substrate for the active site ii. Noncompetitive inhibition • A molecule binds to a site on the enzyme that is distinct fr om the active site F. Some enzymes are controlled by allosteric regulation i. Allosteric regulation • Activate or inhibit enzymes • The number of enzyme molecules being activated (or inhibited) is proportional to the numbers of activator (or inhibitor) molecules that are present at any given time ii. Feedback inhibition • Causes a metabolic pathway to stop producing tis end product when the product concentration reaches an optimal level G. Poisons, drugs and environmental conditions influence enzyme activity i. Poisons and drugs acting on enzymes usually inhibit them, either competitively or noncompetitively H. Some poisons and drugs are competitive or noncompetitive inhibitors of enzymes i. Competitive inhibitors of enzymes permanently block the active site of the enzyme acetylcholinesterase , which breaks down acetylcholine I. The activity of enzymes is influenced by their environment i. Denatured • The enzyme loses the exact three-dimensional structure required for it to function properly ii. Temperature effects the rate of enzyme-catalyzed reactions • Slowed by lower temperature • Accelerated by moderately higher temperatures 5 Date CAPTURING SOLAR ENER GY: PHOTOSYNTHESIS 1. WHAT IS PHOTOSYNTHSI S i. Photosynthesis • The process by which light energy is captured and stored as chemical energy in the bods of organic molecules B. Leaves and Chloroplast are adaptations for photosynthesis i. Epidermis • Protects the inner parts of the lead while allowing light to penetrate ii. Cuticle • A transparent, waxy, waterproof covering that reduces the evaporation of water from the leaf iii. Stoma • Adjustable pores in the epidermis • How the leaf obtains CO2 (necessar y for photosynthesis)? iv. Mesophyll • Most chloroplasts are located v. Vascular bundles • Form veins in the leaf, supply water and minerals to the leaf’s cells and carry the sugars produced during photosynthesis vi. Bundle sheath cells • Cells that surround the vascular b undles • Lack chloroplast in most plants vii. Chloroplasts • Photosynthesis in plants takes place within the chloroplasts • Most contained within mesophyll cells viii. Stroma • Chloroplasts are organelles that consist of a double outer membrane enclosing a semifluid substan ce ix. Thylakoids • Embedded in the stroma • Disk-shaped, interconnected membranous sacs • Each of these sacs encloses a fluid -filled region called the thylakoid space C. Photosynthesis consists of the light reactions and the Calvin Cycle i. Photosynthesis reaction • 6 CO2 + 6 H2O + light energy = C6H12O6 (sugar) + 6 O2 ii. photosynthesis actually occurs in dozens of individual reactions • two distinct stages a. Calvin Cycle b. The light reactions iii. Light reactions • Chlorophyll and other molecules embedded in the membranes of the chloroplast thylakoids capture sunlight energy and convert some of it into chemical energy stored in the energy -carrier molecule ATP (adenosine triphosphate) and NADPH (nicotinamide adenine dinucleotide phosphate) • Water is split apart, and oxygen gas is released a s a by-product iv. Calvin Cycle • Enzymes in the fluid stroma that surrounds the thylakoids use CO2 from the atmosphere and chemical energy from the energy -carrier molecules to drive the synthesis of a three carbon sugar that will be used to make glucose v. Photosynthesis • “photo” refers to the part that captures light energy by the light reactions in the thylakoid membranes • “synthesis” refers to the Calvin Cycle , which captures carbon and uses it to synthesize sugar, powered by energy provided by ATP and NADPH 2. THE LIGHT REACTION: HO W IS LIGHT ENERGY CO NVERTED TO CEMICAL ENERGY i. The light reactions capture the energy of sunlight, sotring it as chemical energy in two different energy-carrier molecules a. ATP b. NADPH B. Light is captured by pigments in chloroplasts i. Electromagnetic spectrum • Ranges from short-wavelength gamma rays, through ultra -violet, visible, and infared light, to very long wavelength radio waves. 2 ii. Photons • Light and other electromagnietic waves are composed of individual packets of energy called photons • Energy corresponds to its wave length a. Short-wavelength – very energetic b. Long-wavelengths – low energy iii. Chlorophyll a • The key light capturing pigment molecule in chloroplasts strongly absorbs violet, blue, and red light, but reflects green, thus giving leae s their green color iv. Accessory pigment • Absorb addistional wave lengths of light energy and trasger their energy to chlorophyll a. • Include chorophyll b o Slights different form of cholorphyll that absorbs some of the blue and redorange wavelengths of light th at are missed by chlorophyll a and reflects yellow-gren light v. Carotenoids • Accessory pigments found in all chloroplasts • Absorb blue and green light and appear mostly yellow or oranage because they reflect these wavelengths C. The light reactions occur in as sociation wirh the thylakoid membrane i. Photosystmes • Each consisting of a cluster of chlorophyll and accessory pigment molecules surrounded by various proteins • Two photosystems – photosystem I and photosystem II – work together during light reaction ii. Electron transport chain • Consosts of a series of electron -carrier molecules embedded in the thylakoid membrane • Within the thylakoid chain a. Photosystem II b. Electron transport chain II c. Photosystem I d. Electron transport chain I e. NADP+ D. Photosystem II uses light energy to create a hydrogen Ion Gradient and to split water 3 a. The energy hops from one pigment molecule to the next until it is funneled into the photosystem II reaction center b. the reaction center of each photosystem consists of a pair of specialized chlorophyll a molecules and a primary electronic acceptor molecule embedded in a complex of proteins i. when the energy from light reaches the reaction Center, it boosts an electron from one of the reception center chlorophylls to the primary electronic acceptor , whic h captures the energized electrons c. the reaction center of photosystem II must be supplied continuously with the electrons to replace those that are boosted out of it when energize by light i. these replacement electrons come from water d. water molecules are split buying enzyme associated with photosystem II, liberating electrons that will replace those lost by the reaction center chlorophyll molecules. i. Splitting water also releases two hydrogen ions (H+) that are used in forming the H+ gradient that drives A TP synthesis ii. for every two water molecules split, one molecule of O2 is produced iii. once the primary electronic acceptor in photosystem II captures the electron, it passes the electron to the first molecule electron transport chain II e. the electrons then t ravels from one electron carrier molecule to the next, losing energy as it goes. i. Some of this energy is harnessed to pump H+ across the thylakoid membrane into the thylakoid space, where it will be used to generate ATP f. finally, the energy depleted electr on leaves electron transport chain II and enters the reactions center of photosystem I, where it replaces the electronic injected when light strikes photosystem I E. photosystem I generates NADPH I. meanwhile, life has also been striking the pigment molecules of photosystem I. this light energy is passed to a chlorophyll a molecule and the reaction center. a. Here, it energizes an electron that is absorbed by the primary electron acceptor of photosystem I i. from the primary electron acceptor of photosystem I, t he energized electron is passed along electron transport chain I 4 b. until it reaches NADP+. i. When an NADP+ molecule ( dissolved in the fluid stroma) picks up two energetic electrons along with one hydrogen ion, the energy carrier molecule NADPH is formed F. The hydrogen ion gradient generates ATP by Chemiosmosis i. chemiosmosis • a process of how electrons move through the thylakoid membrane and use their energy to create and H+ gradient that drives ATP synthesis a. as an energized electron travels along the electron transport chain II, some of the energy of the electron liberates is used to pump H+ into the thylakoid space, creating a high concentration of H+ inside the space b. and a low concentration and the surrou nding stroma i. during chemiosmosis, H+ flows back down its concentration gradient through a special type of channel (ATP synthase) that spans the thylakoid membrane. ii. ATP synthase • Generates ATP from ADP and phosphate dissolved in the stroma as the H+ flows through the channel. 3. THE CAVIN CYCLE: HOW IS CHEMICAL ENERGY S TORED IN SUGAR MOLECULES i. Carbon fixation • Nearly all is performed by photosynthetic organisms • The carbon is captured from the atomospheric CO2 during the Calvin Cycle using energy from sunlight ha rnessed during the light reactions. • B. The Calvin cycle captures cabon dioxide i. Calvin cycle • Often referred to as the C3 pathway a. Carbon fixation b. The synthesis of G3P c. The regeneration of RuBP that allowed the cycle to continue ii. Carbon fixation • Carbon from CO2 is incorporated into larger organic molecules iii. Rubisco • This enzyme combines three CO2 molecules with three RuBP molecules to produce three unstable six -carbon molecules that immediately split in half, 5 forming six molecules of phosphoglyceric acid (PGA, a t hree carbon molecule iv. The synthesis of G3P • Occurs via a series of reactions using energy donated by ATP and NADPH (generated by the light reactions) • During these reactions, six 3 -carbon PGA molecules are rearranged to form six 3-carbon G3P molecules • Three molecules of RuBP are regenerated from five of the six G3P molecules; this regenerations is powered by ATP generated during the light reactions • The single remaining G3P molecule, the end product of photosynthesis, exits the Calvin Cycle v. Photorespiration • Prevents the Calvin Cycle from synthesizing sugar, effectively derailing photosynthesis vi. C4 Pathway and the Crassulacean Acid Metabolism (CAM) pathway • Small percentage of Earths terrestrial plants have evolved biochemical pathways that consume a bit more ener gy, but increase the efficiency of carbon fixation in hot dry climates C. Carbon Fixed during the Calvin Cycle is used to synthesize glucose i. In reactions that happen outside the calvin cycle, two G3P molecules can be combined to form one six-carbon glucose molecule. ii. Glucose can then be used to synthesize sucrose, a disaccharide storage molecule consisting of a glucose linked to fructose. iii. Glucose molecules are linked together in long chains to form starch 6 HARVESITING ENERGY: GLYCOLYSIS AND CELLU LAR RESPIRATION 1. HOW DO CELLS OBTAIN ENERGY? i. Second law of their dynamics • every time a spontaneous reaction occurs, the amount of useful energy in a system decreases and he is produced B. photosynthesis is the ultimate source of cellular energy a. glucose breakdown begins with glycolysis in the cell cytosol, liberating small quantities of ATP b. the end product of glycolysis is further broken down during cellular respiration in mitochondria, s upplying far greater amounts of energy in ATP c. in forming ATP during cellular respiration, cells use oxygen and liberate both water and carbon dioxide - the raw material for photosynthesis ii. photosynthesis • 6 CO2 + 6 H2O + light energy à C6H12O6 + 6O2 iii. complete glucose breakdown • C6H12O6 + 6 O2 à 6 CO2 + 6 H2O + ATP energy + heat energy C. Glucose is a key energy storage molecule i. glucose breakdown • occurs in stages, starting with glycolysis and proceeding to fermentation in the absence of oxygen, and to cellular respiration is oxygen is available 2. WHAT HAPPENS DURING GLYCOLYSIS i. glycolysis • splits the six carbon glucose molecule into two molecules of pyruvate. • Hasn’t Has an energy investment stage and an energy harvesting stage, each with several steps a. during the energy investment stage, phosphate groups and energy from each of two ATP are added to glucose to produce fructose biphosphate b. Fructose biphosphate is broken down into G3P molecules c. During the energy harvesting stage, the two G3P molecules are convert ed into two molecules of pyruvate, generating a total of four ATP molecules and two NADH molecules d. Glycolysis has a net energy yield of two ATP molecules and two NADH molecules 3. WHAT HAPP ENS DURING CELLULAR RESPIRATION i. Cellular respiration • Breaks down the two pyruvate molecules into six carbon dioxide molecules and six water molecules • During this process, the chemical energy from the two pyruvate molecules is used to produce 32 ATP ii. Mitochondria • Organelles that are sometimes called the “powerhouses of the cell” • Has two membranes o Inner membrane encloses a central compartment containing the fluid matrix o Outer membrane surrounds the organelle, producing an intermembrance space between the two membranes B. During the first stage of cellular respiration, Pyruvate is broken down C. During the second stage, high energy electrons travel through the Electron Transport chain D. During the third stage, Chemiosmosis Generates ATP E. Cellular respiration a. In the mitochondrial matrix, each pyruvate m olecule is converted into acetyl CoA, producing one NADH pe r pyruvate molecules and releasing one CO2 b. As each acetyl CoA passes through the Krebs cycle, its energy is captured in one ATP, three NADH, and one FADH2. The carbons of acetyl CoA are released in two CO2 molecules c. During matrix reactions, two pyruvate molecules produced from glucose during glycolysis are completely broken down, yielding two ATP and 10 high energy electron carriers: eight NADH and two 2 FADH2. The carbon atoms from pyruvates are released in six molecu les of CO2 d. The NADH and FADH2 molecules donate their energetic electrons to the ETC embedded in the inner mitochondrial membrane e. As they pass t hrough the ETC , high energy electrons release energy that is harnessed to pump H+ into the intermembra ne space f. As they leave the ETC, the energy -depleted electrons combine with the electron acceptor oxygen and hydrogen ions to form water g. During chemiosmosis, hydrogen ions in the intermembrane space flow down their concentration gradient through ATP synthase channe ls. The complet e breakdown of glucose yields 32 ATP via chemiosmosis F. Cellular respiration can extract energy from a variety of molecules i. Fats are an excellent source of energy, and serve as the major energy-storage molecule in animals ii. To release this energy: a. fatty aci ds are combined wi th CoA b. Then broken down to produce acetyl CoA molecules, which enter the first stage of the Krebs cycle 4. WHAT HAPPENS D URING FERMENTATION i. Anaerobic • No oxygen • Scientists hypothesize that the earliest forms of life appeared under the anaerobic conditions that existed before photosynthesis evolved and enriched the air with oxygen ii. Opportunists • Use fermentation when oxygen is absent, but switch to cellular respiration when oxygen is available B. Fermentation Allows NAD+ to be recycled when oxygen is absent i. Fermentation • Under anaerobic • The second stage of glucose breakdown • During this pyruvate in the cytosol is converted either into lactate, or into ethanol and CO2 ii. Aerobic • No oxygen 3 • Under this condition, most organisms use cellular respiration , regenerating NAD+ by donating the energetic electrons from NADH to the electron transport chain • Under these conditions, with no oxygen to allow the ETC to function, the cell must regenerate the NAD+ using fermentation • During fermentation, the electrons from NADH (along with some hydrogen ions) are donated to pyruvate, changing the pyruvate chemically. • Fermentations seems to waste energy in NADH, because this energy is not used to generate ATP iii. Organisms use one of two types of fermentation to regenerate NAD+ • Lactic acid fermentation o Produces lactic acid from pyruvate • Alcoholic fermentation o Generates alcohol and CO2 from pyruvate C. Some cells ferment pyruvate to form lactate i. Lactic acid fermentation • Fermentation of pyruvate to lactate ii. When muscles are sufficiently low on oxygen they rely on glycolysis to supply its meager two ATP per glucose molecule • May provide the energy need ed for a final, brief burst of speed • Muscles then ferment the resulting pyruvate molecule to lactate, using fermentation from NADH and hydrogen ions iii. As oxygen is replenished • Lactate is converted back into pyruvate in muscle cells, where it will be used for cellular respiration, and also in the liver, where the pyruvate is converted back to glucose • This glucose may then be stored as glycogen or released back into the bloodstream and distributed to cells th roughout the body iv. A variety of microorganisms use lac tic acid fermentation D. Some cells ferment pyruvate to form alcohol and carbon dioxide i. Alcoholic fermentation • Many microorganisms engage in this under anaerobic conditions • during this fermentation pyruvate is converted into ethanol and CO2 (rather than lactate) • This releases NAD+, which is then available to accept more high-energy electrons during glycolysis 4 5


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