Exam 4 Bio 1107 - Summary Principles of Life PDF

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Section and Chapter Summaries. Professor Dolan...

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Exam 4 April 26th Chapter Notes: Concept 2.3 Carbohydrates Consist of Sugar Molecules ● Carbohydrates contain carbon bonded to hydrogen and oxygen. ● Monosaccharides include pentoses (with five carbons) and hexoses (with six carbons). ● Glycosidic linkages are covalent bonds between saccharides. Disaccharides such as sucrose each contain two monosaccharides, whereas polysaccharides such as starch and cellulose contain long chains of monomers. Concept 2.5 Biochemical Changes Involve Energy ● A chemical reaction occurs when atoms have sufficient energy to combine or to change their bonding partners. ● Anabolic reactions require energy and are endergonic. Catabolic reactions release energy and are exergonic. ● The laws of thermodynamics govern biochemical reactions. The first law states that in any transformation, energy is neither created nor destroyed. The second law states that useful energy tends to decrease. In other words, entropy (disorder) tends to increase. Concept 6.5 During Photosynthesis, Light Energy Is Converted to Chemical Energy ● The light reactions of photosynthesis convert light energy into chemical energy. They produce ATP and reduce NADP+ to NADPH. ● Light is a form of electromagnetic radiation. It is emitted in particle-like packets called photons but has wavelike properties. Molecules that absorb light in the visible spectrum are called pigments. Photosynthetic organisms have several pigments, most notably chlorophylls. ● The absorption of a photon puts a chlorophyll molecule into an excited state that has more energy than its ground state. This energy can be transferred via other chlorophylls to one in the reaction center of a photosystem. ● An excited chlorophyll can act as a reducing agent, transferring excited electrons to other molecules. Oxidized chlorophyll regains electrons by the splitting of H2O. ● In the thylakoid membrane of the chloroplast, photosystems I and II and a noncyclic electron transport system produce ATP via oxidative phosphorylation. NADPH and O2 are also produced. Cyclic electron transport uses only photosystem I and produces only ATP.

Concept 6.6 Photosynthetic Organisms Use Chemical Energy to Convert CO2 to Carbohydrates ● The Calvin cycle makes carbohydrates from CO2. The cycle consists of three processes: fixation of CO2, reduction and sugar production, and regeneration of RuBP. ● RuBP is the initial CO2 acceptor, and 3PG is the first stable product of CO2 fixation. The enzyme rubisco catalyzes the reaction of CO2 and RuBP to form 3PG. ● ATP and NADPH formed by the light reactions are used to fuel the reduction of 3PG to form glyceraldehyde 3-phosphate (G3P)—a starting material for the synthesis of glucose and other carbohydrates. Concept 3.3 Some Proteins Act as Enzymes to Speed up Biochemical Reactions ● A chemical reaction must overcome an energy barrier to get started. An enzyme is a catalyst that affects the rate of a biological reaction by lowering the activation energy needed to initiate the reaction. ● A substrate binds to the enzyme’s active site—the site of catalysis—forming an enzyme–substrate complex. Enzymes are highly specific for their substrates. ● At the active site, a substrate enters its transition state, and the reaction proceeds. ● Substrate binding causes many enzymes to change shape, exposing their active site(s) and allowing catalysis. ● Some enzymes require non-protein “partners” called cofactors to carry out catalysis. ● Substrate concentration affects the rate of an enzyme-catalyzed reaction. At the maximum rate, the enzyme is saturated with substrate. Concept 6.1 ATP and Reduced Coenzymes Play Important Roles in Biological Energy Metabolism ● Metabolism is carried out in small steps and involves coenzymes as carriers of chemical energy. ● Adenosine triphosphate (ATP) serves as “energy currency” in the cell. Hydrolysis of ATP releases a large amount of free energy. ● In oxidation, a material loses electrons by transfer to another material, which thereby undergoes reduction. Such redox reactions transfer large amounts of energy. ● The coenzyme nicotinamide adenine dinucleotide (NAD) is a key electron carrier in biological redox reactions. It exists in two forms, one oxidized (NAD+) and the other reduced (NADH).

Concept 6.2 Carbohydrate Catabolism in the Presence of Oxygen Releases a Large Amount of Energy ● The sequential pathways of aerobic glucose catabolism are glycolysis, pyruvate oxidation, and the citric acid cycle. ● In glycolysis, a series of ten enzyme-catalyzed reactions in the cell cytoplasm converts glucose to two molecules of pyruvate. Energy is released and captured as ATP and NADH. ● The next pathway, pyruvate oxidation, links glycolysis to the citric acid cycle. Pyruvate oxidation converts pyruvate into the two-carbon molecule acetyl CoA. ● In the citric acid cycle, a series of eight enzyme-catalyzed reactions fully oxidizes acetyl CoA to CO2. Much energy is released, and most is used to form NADH. ● The energy in NADH is used to make ATP via a series of electron transport carriers and chemiosmosis. ● In oxidative phosphorylation, ATP is formed with the energy derived from the reoxidation of reduced coenzymes. This depends on the process of chemiosmosis, in which a proton gradient across a membrane powers ATP formation. This occurs at the cell membrane in prokaryotes, and in the mitochondria and chloroplasts in eukaryotes. Concept 2.4 Lipids Are Hydrophobic Molecules ● Fats and oils are triglycerides, composed of three fatty acids covalently linked to glycerol. ● Saturated fatty acids have hydrocarbon chains with no double bonds. Unsaturated fatty acids contain double bonds in their hydrocarbon chains. ● Phospholipids contain two fatty acids and a hydrophilic, phosphate-containing polar group attached to glycerol. They are amphipathic, with both polar and nonpolar ends. They form into a structural bilayer in water. Concept 6.4 Catabolic and Anabolic Pathways Are Integrated ● The catabolic pathways for the breakdown of carbohydrates, lipids, and proteins feed into the energy-harvesting metabolic pathways. ● Anabolic pathways use intermediate components of the energy-harvesting pathways to synthesize fatty acids, amino acids, and other essential building blocks. ● The formation of glucose from intermediates of glycolysis and the citric acid cycle is called gluconeogenesis. ● The enzymes of glycolysis and the citric acid cycle are regulated by various mechanisms, including allosteric regulation. Excess acetyl CoA is diverted into fatty acid synthesis.

Class Notes/ Lecture: April 1st Identify the immediately preceding source of carbon for that component: Cheeseburger - Burger pattie: getting its carbon from the grass that the cows eat - Getting carbon source from the plants that produce that carbon Animals get energy and mass to build and maintain their bodies by eating plants (or animals that ate plants) Jan van Helmont’s Experiment (early 17th century) WRONG HYPOTHESIS IF Plants get mass from soil AND A willow is planted in a pot with a known amount of soil and allowed to grow THEN What would you expect to see if the hypothesis is supported? TH 28.2 If plants get their mass from the soil and a willow is planted in a known amount of soil and allowed to grow, then... - As the plant mass increases, the soil mass should decrease We should know that the “soil hypothesis” was wrong. Plants can grow without soil=hydroponics Farmers harvest hay every year but don’t run out of dirt

PLANTS GET THEIR MASSES FROM CARBON FROM THE AIR Where are plants getting the carbon to generate cellulose? PHOTOSYNTHESIS - Trees (and other plants) are made out of carbon to get from the atmosphere (CO2) All living things (including plants themselves!) use that carbon and associated energy to grow, develop, and live (ie. maintain homeostasis) CELLULAR RESPIRATION -

In light (no water), neither photosynthesis nor cellular respiration was active. 2g → 1.96g In light and water condition, both photosynthesis and cellular respiration was active 2g → 2.63g - In water (no light), cellular respiration was active. 2g → 1.70g The plants lose mass in the water no light experiment because They are not gaining carbon through photosynthesis and they are losing carbon through cellular respiration. You need growth to get photosynthesis. You need water for cellular respiration. Nothing will happen if you do not have water.

Cellular respiration: water Photosynthesis: first water and then growth, and light

April 3rd How do seeds accumulate biomass (ie. grow) Photosynthesis: 1. Light reaction converts light energy to chemical energy in the form of ATP and NADPH 2. Carbon fixation reaction uses energy from ATP and NADPH to “fix” or reduce carbon from the CO2 to carbohydrates (eg. glucose)

Photosynthesis takes place in the chloroplast

The light-dependent reactions use light energy to make two molecules needed for the next stage of photosynthesis: the energy storage molecule ATP and the reduced electron carrier NADPH. In plants, the light reactions take place in the thylakoid membranes of organelles called chloroplasts.

Zoom in on a thylakoid: STEPS... Light + H2O are used as reactants for the light-dependent component of photosynthesis • Light excites Photosystem II (PSII, also known as P680), which makes it a strong oxidizing agent • PSII oxidizes H2O, which means H2O gets oxidized • In your groups, come up with an explanation of what it means when something is “oxidized” REFRESHER ON OXIDATION AND REDUCTION (REDOX) • When H2O gets oxidized, what gets formed? Where does that go?

Transfer of electrons down a series of proteins called an “electron transport chain,” which pumps H+ (protons) out of the stroma and into the inside of the thylakoid • Compare [H+] inside the thylakoid vs. in the stroma to as a result of all of this – where is [H+] higher? • Where is pH lower? • Photosystem I (PSI, aka P700) accepts electrons and is also excited by light • PSI then donates its electron to NADP+ to form NADPH (an “energy storage” molecule) • Is NADP+ oxidized or reduced? How can you tell? • [H+] flows down concentration gradient through ATP synthase to form ATP (more on this later) • Result of this is transformation of light energy to chemical energy in the form of ATP and NADPH The herbicide atrazine inhibits the function of photosystem II. Working in your groups, predict what effect would this have on: • The [H+] gradient • NADPH levels • ATP synthesis

Photosystem 2: hydrolyzes the water and takes in light Photosystem 1 takes in light and produces NADPH and throught ATP sythase ATP is produced. ATP is able to be produced through the gradient that the photosystems. If photosystem 1 isnt working photosystem 2 can still produce H+ and then have the same gradient and ATP sythase output. Step 5 as a whole wants equilbrium.

April 5th 1. What is the main purpose/ outcome of the light dependent reaction in photosynthesis? - You make ATP and NADPH 2. When H20is oxidized during the light dependent component of photosynthesis, what is formed? Oxygen gas and hydrogen ions 3. The herbicide paraquat inhibits the function of photosystem I. What immediate effect would this have on a) H+ gradient, b) NADPH levels and c) ATP synthesis? a. Nothing, b. Decrease c. Nothing Carbon fixation reaction uses energy from ATP and NADPH to “fix” (or reduce) carbon from CO2 to carbohydrates (e.g., glucose)

CALVIN CYCLE ATP and NADPH generated in the light reaction = energy sources to drive the Calvin cycle, which is the fixation of carbon (transformation from gas to usable form) Takes place in the stroma (why does this make sense?) The carbon in 3PGA gets… reduced When the carbon in 3PGA is reduced, the following molecule is oxidized… NADPH Endergonic reactions… Require the input of energy and have a positive delta G

April 8th 1. What is the overarching purpose of the Calvin Cycle? -converting energy - take a complex form of carbon and convert it to a useable form - to fix carbon means to reduce carbon 2. What happens to the top carbon between 3-PGA → G3P? How can you tell -being reduced because it gained an electron -gaining a hydrogen being reduced 3. What molecules get oxidized? How can you tell? -gaining an electron 4. Forming G3P from 3PGA is “endergonic” what allows this reaction to proceed? ATP The input of energy Free energy drops from ATP to ADP + Pi △G°=-30 kJ/mol ATP hydrolysis: ATP + H2O → ADP + Pi + energy Energy is used to reduce carbon Why is it so energetically favorable for ATP to lose its terminal (end) phosphate group? Electrostatic repulsion (the negative sign) AND Entropy This is why ATP is considered the main “energy currency” or energy storage for cells.

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Here is an “energy diagram” also known as a progress curve ATP + H2O = reactants ADP + Pi = products Negative charge on the phosphates repels H2O Have to “get over” this somehow

So why is ATP not hydrolyzed to ADP all the time? - Enzymes that catalyze. ATP hydrolysis reaction have R groups that stabilize negative charge on phosphates - Lowers activation energy This is what enzymes do! Photosynthesis fixes carbon to produce glucose, capturing energy in chemical form... Then what? - Glucose is transported in multicellular organisms or simply diffuses in single-celled organisms to sites where it is used = glycolysis!

April 10th 1. The conversion of ATP + H20→ ADP to Pi (aka inorganic phosphate) is energetically favorable or unfavorable? Favorable- spontaneous. Energy is released. 2. Which means Delta G for the reaction positive or negative? Negative- when a reaction is favorable. Higher G to a Lower G 3. Which means its energy diagram/ program curve should look like? Downward slope, negative 4. So why is ATP not hydrolyzed (cut with water) to ADP all the time? Because of Activation Energy: that hill that is has to jump over. It keeps it from being hydrolyzed all the time 5. How would the ATP → ADP energy diagram/ progress curve change in the presence of an enzyme that catalyzes the hydrolysis of ATP? It will lower the need for activation energy. (The hump will go away) GLYCOLYSIS Lysis: cutting Step 1 of Glycolysis Once glucose is taken up into a cell, a phosphate group is added. Kinase: enzyme that adds a phosphate • This traps glucose in the cell (can’t fit through glucose transporter) • What does the name of the enzyme indicate about its function? HEXO- 6 CARBON SUGAR • Is energy being consumed or harvested? We are using energy. High energy to low energy. Because we added phosphate.

• Energy from hydrolysis of ATP drives this reaction forward = reaction coupling (one way to turn a rxn with +△G into one with -△G ) Adding the phosphate is unfavorable because of the charge Phosphate is acting here as a “functional group” Or collection of atoms responsible for the characteristics of a molecule Step 2 of Glycolysis The enzyme that carries this out is called an “isomerase” why does this make sense? Changing the structure Energetically favorable to separate because of the charge. Step 3 of Glycolysis ATP to ADP- you are adding that phosphate. From High energy to Low energy Use energy. Step 4 of Glycolysis Split the 6 carbon to a 3 carbon molecule Step 5 of Glycolysis What do you notice: they are isomers What kind of enzyme should catalyze: isomerase Why bother? It is produced through photosynthesis. It is the only one to continue through glycolysis because of its shape. Only GAP can proceed through glycolysis It wants to re-establish equilibrium. Based on Le Chatelier’s principle. *** look up Step 6 of Glycolysis Harvesting because it acts like energy storage - Coming from the oxidation of carbon Step 7 of Glycolysis harvesting - Oxidation of carbon REVIEW QUESTIONS: 1. Compare the red and blue carbons which is more oxidized? How do you know? - CO- blue is more oxidized because the addition of Hydrogen to the red carbon means that Carbon is being reduced 2. Is the Delta G under of an unfavorable reaction positive and negative? - Positive because it is going from low G to high G. It needs energy to go forward 3. What is the one way to “drive” an unfavorable reaction forward? - Reaction coupling - Not an enzyme it just decides how fast it will go. 3 steps: These are regulated LOOKUP 1, 3, 10 PEP is higher energy than ATP -hydrolysis of ATP Going to be negative delta G overall

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Regulation of glycolysis occurs at three points of the pathway. These correspond to the steps with the largest negative free energy changes (i.e. most exergonic - negative ΔG). The magnitude of the ΔG for these steps makes them essentially irreversible. The most important point of control is at the reaction catalyzed by phosphofructokinase (PFK, Reaction 3 ) Other control points are the hexokinase (Reaction 1) and pyruvate kinase (Reaction 10) reactions.

April 15 Final product: Pyruvate to Acetyl CoA - Harvested energy because the NAD+ to NADH - We lost CO2 - CO2- fully oxidized carbon - Where does CO2 go? Meet Coenzyme A (aka CoA) and acetyl CoA • Coenzymes (like CoA) are molecules that are not enzymes or proteins themselves but are important for enzymes to function • Acetyl CoA = CoA + acetyl group • Acetyl CoA shuttles carbons between many metabolic pathways - Acetyl CoA acetyl group = methyl group (-CH3) +carbonyl (-C=O) - Shorthand for the coenzyme A molecule is HS-CoA (CoA is everything in the red box above) April 17 1. Order the following from C being the most to least oxidized: C-C, C-O C-H, C-S C-O, C-S, C-C, C-H - For oxidation, you want to have a bond that the atom has a high electronegativity like oxygen 2. Step 8, what reaction is happening? Oxidized because you lost your hydrogens 3. Step 8 is Harvesting energy

Rules of Thumb: ATP→ ADP use energy NAD→ NADH harvest energy ADP→ ATP harvest energy

Gaining Hydrogen= reduction Losing Hydrogen= oxidized

Light cylcle light reactions 2. Calvin cycle Leaves get a lot of chloroplasts 8 1.Name two molecules that donate electrons to the electron transport chain (ETC) and note which complex each reduces. NADH and FADH2

2. Make a simple drawing of a mitochondrion inside a cell(use a circle for each membrane rather than detailed phospholipid bilayers to save time!), then: a. Draw in the 4 complexes of the ETC and ATP synthase b. Draw in arrows to indicate locations and directions H+ is moving- moving toward the intermembrane c. Indicate where [H+] is high and low: high intermembrane and low in the matrix d. Indicate where ATP is being produced.- ATP synthase

3. The drug dinitrophenol makes it possible for H+ to flow freely across membranes. What effect would this have on (a) Electron transport in the ETC, (b) the [H+] gradient, and (c) ATP synthesis? a)decrease you need a gradient to get ATP to form b)decrease because you would no longer need it c)decrease you need a gradient to get ATP to form

1. Carbon and energy enter and exit glycolysis in what form (i.e., which molecules)? What happens to these molecules? Glucose and pyruvate. Creates two ATP, two NADH 2. Carbon and energy enter and exit the citric acid cycle in what form? What happens to these molecules? Acetyl CoA. Makes 3 NADH, 1 FADH2 and 1 ATP 3. Energy enters and exits oxidative phosphorylation (i.e., electron transport chain + ATP synthase) in what form? Enters as NADH and FADH2 and exits as NAD +H+ and FAD 4. Energy enters and exits the light dependent phase of photosynthesis in what form? What happens to these molecules? 5. Carbon and energy enter and exit the Calvin cycle in what form? What happens to these molecules?

Quizzes Carbohydrates contain: carbon, oxygen, hydrogen Examples of polysaccarides: Starch, glycogen. Cellulose The Carbon source for photosynthesis is: CO2 During photosynthesis, light energy is initally captured by: excitation of electrons in chlorophyll The light dependent reactions of photosynthesis produce the following- storing compounds: ATP and NADPH The conversion of NADP+ to NADPH is… reduction In the Calvin Cycle, ATP transfers one of its phosphate groups to generate RuBP. The process - of transfering ...