Exam 3 prelec and notes - Wischusen PDF

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1 Exam 3: Photosynthesis Dr. Wischusen Photosynthesis Overview Photosynthesis → major energy transformations ● 6CO2+ 12H2O + Light → 6O2 + C6H12O6 + 6H2O ○ Convert two low energy molecules into a high energy molecule ○ Water molecules on either side of equation ○ Can be balanced ○ Carbon and oxygen in CO2 will go in glucose ● Two Stage Process ○ Capture light energy in chemical energy (light reactions) ○ Use the chemical energy to convert CO2 into glucose (Dark Reactions) (Calvin Cycle) ● All carbon and oxygen in glucose come from CO2 ● Hydrogen in water → how it is used in photosynthesis ○ Half go into old water molecules, half into new water molecules ■ Water is the source of electrons ■ 12 H2o is different from 6 H2o ○ Oxygen in two places on Reactant side, three places in Product side ■ What is the fate of the oxygen in water? ● It becomes a part of oxygen ■ Oxygen is the byproduct of the product, the plant does not want it ● Enables breathing for humans ■ Convert 2 low energy molecules Inputs: CO2, Water, Light Outputs: oxygen, glucose, water Photosynthesis is a Two stage process Photosynthetic structures ● Chloroplasts ● Thylakoid membranes: disks of membranes that are stacked ○ Third membrane system ○ Granum: stack of thylakoids ● Stoma: liquid portion of inside chloroplast but outside of thylakoid Where did most of the mass (dry weight) of this tree come from? (think photosynthesis) ● Air ○ Air is full of molecules ○ Plants take the molecules and combine them together → making a tree Chloroplast

2 Exam 3: Photosynthesis Dr. Wischusen Structure of the chloroplast ● Two outer chloroplast membranes ● Stroma: liquid portion inside of the chloroplast ○ Contains: calvin Cycle, thylakoid membranes, hydrogen ion gradient ● Inner membrane system: thylakoid membranes ○ Thylakoid: third membrane, disks of membrane like figures that can stack ■ Stacked thylakoids are called a granum ○ Atp Synthase is IN the thylakoid Dark Reactions → Calvin Cycle Using the chemical energy to convert CO2 into glucose → Dark Reactions or Calvin Cycle ● Gain ATP and NADH ● Give off reduced ADP and NADP Calvin Cycle → Dark Reactions ● Endergonic → requires energy ○ Required energy: light ● The process → Every step is enzyme catalyzed ● Does NOT directly require light ○ Indirectly requires light ○ Cannot happen at night Where do we get the converted light energy to power the Calvin cycle? ● Light reactions ● Cyclic and noncyclic - photophosphorylation The Process of the Calvin Cycle ● Inputs CO2 → joins to a 5- carbon intermediate that's in the cycle → making a 6 carbon molecules ● Breaks down into two 3- carbon molecules ● Converts atp to adp → Adds energy to 3 carbon molecules ○ Input: ATP ○ Output: ADP ● NADPH+H+ → NADP+ ○ Input NADPH+H+ ○ Output: NADP+ ■ Reduction ■ Adding energy ○ output G3P ■ 2 G3P make glucose ● Some molecules stay in the cycle ● Input ATP (output ADP), convert five 3-carbon molecules to three 5-carbon molecules ● Dark photosynthesis→ Complete

3 Exam 3: Photosynthesis Dr. Wischusen ●

What are the inputs of the Calvin Cycle? ● CO2, ATP, NADPH+H+ ● Co2 is converted to make glucose → Needs energy to do so ● ATP and NADPH + H+ → High energy molecules What are the outputs of the Calvin Cycle ● ADP, NADP+, G3P ● ADP and NADP+ → Oxidized, less energetic forms of the energy that was input ● G3P → Glyceraldehyde 3 Phosphate Calvin Cycle: overview ● Phase 1: Carbon Fixation ○ Input (3) CO2 ● Phase 2: Reduction ○ Redox (6) ATP → (6) ADP ○ Redox (6) NADPH → (6) NADP ○ Releases 6 phosphate ○ output → G3P ● Phase 3: generation of the CO2 acceptor ○ Output ○ G3P At night, which of the following molecules would be expected to increase in concentration inside the stroma of the chloroplast

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NADP Cannot make NADPH+H+ because there is no energy Calvin Cycle will take remaining NADPH+H+ and ATP and use it ○ Calvin cycle outputs NADP and ADP ○ Oxygen level and G3P will decrease because there is no light energy to be transferred from noncyclic to the Calvin Cycle

Light reactions → Cyclic and Non-Cyclic Phosphorylation Capturing light energy in chemical energy → light reactions ● Endergonic → sunlight is the energy source that helps to conduct the reaction ○ Needs light energy to produce ● Produce High energy molecules, atp, ● Gain reduced form of NADP+ and ADP+ ● Produces high energy molecules are used to power the calvin cycle Cyclic and noncyclic photophosphorylation ● “Photophosphorylation” → using light to add a phosphate group to make ADP to make ATP ● “Cyclic” and “noncyclic” → Dependant on the movement of electrons ○ In one case we cycle electrons (cyclic) ○ Electrons flow through in a non-cyclic manner ○ Can be done simultaneously ● The function of the light reaction is to catch light energy and convert it into chemical energy → Initial step of capturing energy in light is the most important step ○ Energy source: light energy ○ Not converting light into anything, using the energy from the light to energize electrons → electrons power the high energy molecules - Such as ATP and NADPH+H+ ● That energy is then used by the Calvin Cycle to convert carbon dioxide into a sugar ○ G3P

5 Exam 3: Photosynthesis Dr. Wischusen Non- Cyclic Photophosphorylation Noncyclic ● Use light energy to conduct phosphorylation to convert ADP to ATP ● Non cyclic → electrons flow instead of cycle ● ○ Light energy enters→ strikes photosystem II → energy is picked up by pigment molecules → travels through pigment molecules → passes onto the reaction center (P680 in this case) → energizes electrons that are picked up by the electron acceptor → electrons are passed through the cytochrome complex → hydrogen ions are pumped from one side of the membrane to the other→ creates hydrogen ion gradient → makes ATP → electrons flow to the P700 reaction center→ light energy is absorbed in other photon of light energy → passes from pigment molecule to pigment molecule → gets to the reaction center that energizes the electrons → picked up by another electron acceptor → paradoxin (electron acceptor) → electrons used to reduce NADP to NADPH+H+ ● Electrons used originally came from water, now flow through all the way to NADPH+H+ ● Light phosphorylates ADP to ATP ● The process of moving through the cytochrome chain ○ Pump hydrogen ions from stroma, into thylakoids ■ Building up hydrogen gradient ■ Hydrogen continues to pass through the gradient, releasing energy every time ■ This energy is used in the conversion of ADP to ATP ○ ATP and NADPH+H+ that are produced in the noncyclic cycle are used in the Calvin Cycle Photosystem I gave up electrons to NADP+ to make NADPH+H+ ● Gets more electrons coming from the flow of electrons from photosystem II to photosystem I Photosystem II gets electrons from water ● Water gets split into ½ o2 ○ Two electrons and hydrogen ions ● Hydrogen ions stay in thylakoid and eventually flow out to make ATP ● Electrons will be used to replace the electrons lost from photosystem II ● ○ ○ ○ ○ ○ ○ Photosystem II - Energy comes

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in → excites electrons → electrons pass down through cytochrome chain→ pump hydrogen ions from one side of the membrane to the other → electrons flow to photosystem I → electrons are energized by energy from another photon of light → passed on to reduce NADP+ to NADPH+H+ → hydrogen ions come from splitting of water and are pumped across membrane → create a hydrogen ion gradient → hydrogen ions flow out through ATP synthase and give off energy → energy given off allows us to convert ADP to ATP → energy needed for the Calvin cycle Noncyclic electron flow ○ Originally started in H2o ○ Moved to photosystem II → energize electrons ○ Flow to Cytochrome complex or Cytochrome chain ○ Photosystem I → electrons are reenergized ○ Electrons went on to form NADPH+H+ ○ Calvin cycle (dark reactions) Noncyclic inputs and products ○ Inputs: light, H2O, ADP, NADP+ ○ Outputs: O2, ATP, NADPH+H+ ■ Oxygen is a useless byproduct→ therefore it is released

7 Exam 3: Photosynthesis Dr. Wischusen Cyclic Photophosphorylation Cyclic Photophosphorylation ● Only involves photosystem I ● Light energy enters → energy is used to energize electrons in photosystem I → electrons are captured by the primary electron acceptor → pass through the cytochrome change → return to photosystem I → pump hydrogen ions across membrane to make hydrogen gradient → creates energy to make atp Cyclic electron flow ● Photosystem I → one photon of light energy hits pigment molecules → molecules passed to the reaction center → energizes electrons → electrons are picked up by a electron acceptor → passes to cytochrome complex ● Cytochrome complex ● Return to photosystem I Inputs and outputs ● input : light, ADP ● Output: ATP What is/are the outputs of cyclic phosphorylation? ● ATP ● ATP is a direct input to calvin cycle ● Electrons cycle→ water is not needed ● Photosystem I → pigment molecules → primary acceptor →cytochrome complex → gains energy from light → back to photosystem one ○ Hydrogen ions are pumped from outside of thylakoid to the inside (creating gradient) , then pumped back out going through ATP synthase (creating more ATP) ● As those electrons pass through cytochrome complex, they pump hydrogen ions from stroma into the space in the thylakoids that built up a hydrogen gradient, when they flow out of the ATP synthase, they are giving off energy that will be used to convert ADP + P into ATP

Why do we need both pathways ● Need more ATP than NADH+H+ ● Cyclic and noncyclic pathways are regulated by how much NADPH+H+ ○ Not enough NADPH+H+ → cyclic ■ Only produce ATP ○ Enough NADPH+H+ → noncyclic ■ O2, ATP, NADPH+H+

8 Exam 3: Photosynthesis Dr. Wischusen Photosystems Photosystems as a whole ● A collection of several hundred pigment molecules along with some proteins in the thylakoid membrane ● most important part of Photosynthesis is the point at which light energy is captured in some initial form of chemical energy → requires photosystem ● 2 types of photosystems → photosystems I and II Photosystem I and II alike ● Embedded in the thylakoid ○ Similar to molecules in ETC in cellular respiration ○ Can accept and give up electrons ○ Cytochrome complex ○ Electrons can move from one to another→ moving from one photosystem to another ■ Key to how light systems work ■ Use the free flow of electrons to pump hydrogen ■ Reaction center molecules can give up electrons ■ Pigment molecules can absorb light → can’t do anything with it ● Contain Antenna pigments ○ ~ 200 molecules of chlorophyll A ○ ~ 50 molecules of chlorophyll B ○ ~ 50 molecules of other pigments ● Reaction center molecules ○ Special versions of chlorophyll A (P700 or P680) ■ Numbers refer to the wavelength of light that those molecules absorb most effectively ○ Play a pivotal role in how a photosystem functions

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Process of a Photosystem ○ Light comes in → absorbed by pigment molecules → passed around pigment molecules until it reaches a reaction center ○ A reaction center molecule can be used to energize electrons and create a pair of high energy electrons. ■ These electrons are then accepted by a primary electron acceptor ○ At this point, the photosystem is actually beginning to capture the energy of light ■ Until we get it into high energy electrons, we haven’t actually captured the light → but we may not be able to hold onto it ○ Once the light is in the form of high energy electrons → pass through the primary electron acceptor → now the energy is obtained Back to the chloroplast ● Photosystems are embedded in the thylakoid ○ Can be seen as two large green circles ■ Photosystem 2 on the left and 1 on the right. ○ Connected by a series of proteins that can accept or give up electrons → cytochrome chain ■ Similar to ETC in cellular respiration ○ Light energy passes through cell membrane, through the cytoplasm, into the chloroplast and strikes the photosystem ○ The light energy gets captured by a pigment molecules → gets passed around the pigment molecules → reaches reaction center True or False As electrons flow along the thylakoid membrane from the PS II to PS I, they release energy ● True ● Light comes into thylakoid → gets passed from pigment molecule to pigment molecule → ● Pigment gets to reaction center → electrons energized ● Electrons flow downhill down the hydrogen ion transport → release energy ● Hydrogen ions move to ATP synthase → ATP production ● missed ● Water is split into ½ (o2) → gives off electrons Why have so many types of pigments in a photosystem? ● Each different pigment molecule accepts different wavelengths of light ● Accepting a broad variety of antenna pigments, the plant is able to accept a broader surface of wavelengths of light → able to harvest more light ● Absorption spectrum → ● Absorption spectra → ○ Green light is reflected → other colors are absorbed

10 Exam 3: Photosynthesis Dr. Wischusen Three identical plates of radish seeds are incubated under three conditions, with results as show. Their dry weights in increasing order would be?

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3,1,2 - Hint: What happens when people lose weight → exhaled as CO2 Plants do cellular respiration and photosynthesis at the same time 3 has no light→ only doing cellular respiration → lets out CO2 Barely anything is happening with seeds in 1 2 is doing cellular respiration and photosynthesis→ mass will increase because photosynthesis holds more CO2 than respiration

11 Exam 3: Photosynthesis Dr. Wischusen Quiz 16: active photosynthesis 1. What process produces oxygen? a. Photosynthesis i. Uses CO2 to produce “glucose” G3P, produces oxygen ii. Oxygen is a by product of the photosynthetic process b. Cellular respiration i. Inhales oxygen, exhales carbon dioxide 2. Which set of reactions uses H2O and produces O2? a. Light dependent reactions i. Uses energy of light b. Light independent reactions i. Input: co2, atp, NADH+H+ ii. Output: G3P, ADP, NADP 3. What is the importance of the light- independent reactions in terms of carbon flow in the biosphere a. The light independent reactions turn CO2, a gas, into usable carbon in the form of sugars i. Co2 is usable until plants have “fixed” this carbon into sugar 4. True / false: the light- dependent reactions of photosynthesis use water and produce oxygen a. True i. The water molecules are split to replenish electrons in photosystem II, leaving behind protons, which are used to generate a proton gradient for the formation of ATP, and oxygen, which is released as a by-product 5. Which of the following molecules is the primary product of photosystem I? a. NADPH i. The NADPH produced by photosystem I is used to supply energy for the production of sugars during photosynthesis 6. What is the biological significance of the light- independent reactions of photosynthesis? a. They convert carbon dioxide to sugar i. All organisms use the sugars produced by photosynthesis to generate energy 7. Which of the following statements best describes the relationship between the lightdependent and light - independent reactions of photosynthesis? a. The light- dependent reactions produce ATP and NADPH. Which are then used by the light - independent reactions i. Light energy drives the formation of ATP and NADPH during the light dependent reactions; these energy molecules are then used during the light- independent reactions to form sugars 8. Which of the following reactions ensures that the Calvin Cycle (light independent) can make a continuous supply of glucose? a. The regeneration of RuBP ensures that the calvin cycle can proceed indefinitely, since RuBP fixes carbon dioxide into an organic molecule that is used to produce sugar

12 Exam 3: Photosynthesis Dr. Wischusen 9. What molecule is the main product of the Calvin Cycle a. G3P i. Glyceraldehyde 3 phosphate ii. Glucose is discussed as the product of photosynthesis primarily for convenience. Infact, very little free glucose is produced by or transported from photosynthetic cells. 10. What is the basic role of CO2 in photosynthesis a. CO2 is fixed or incorporated into organic molecules i. CO2 is used in the Calvin Cycle to produce G3P 11. Select the most accurate statement describing the basic function of the reactions of photosynthesis a. The basic function of the light reactions of photosynthesis is the conversion of solar energy to chemical energy

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In a light - dependent reaction, light generates high energy molecules such as ATP and NADPH that are given up for the Calvin Cycle, the calvin cycle then returns NADP and ADP

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Nucleic Acids Classes of Organic Molecules ● Carbohydrates ● Lipids ● Proteins ● Nucleic acids Nucleic Acids ● Polymers of nucleotides ○ Large molecules ● Unbranched chains ○ Molecules have directionality Nucleotides ● Building block of nucleic acids ● Structure: 5 carbon sugar ○ Ribose: found in RNA ○ Deoxyribose: found in DNA ● Phosphate group ● Nitrogenous base (5 types) ○ Often refer to nucleotides by their base

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○ 5 carbon sugar is in the middle (on each side) ○ Oxygen on the top corner ○ Nitrogenous Base is attached to the #1 carbon ○ Phosphate attached to the #5 carbon ○ Most important locations: 1,3,5 Joined together by condensation reaction ○ Phosphate group of one nucleotide and the the #3 carbon on the sugar of the next nucleotide Backbone of molecule is sugar and phosphate

5 nitrogenous bases ● Pyrimidines → cytosine, thymine, uracil ○ Single ring structures ○ Cytosine and thymine are found in DNA ○ Uracil found in RNA

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Purines → adenine, guanine ○ double ring structures ○ Adenine and guanine are found in DNA

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Sugars → deoxyribose, ribose ○ Label backwards, start with hydrogenous base and ending with phosphate group ■ Build from 5 prime end towards 3 prime end ○ Ribose has a hydroxyl group → single backbone ■ Adenine ■ Guanine ■ Cytosine ■ Uracil ○ Deoxyribose has a hydrogen → double back bone ■ Adenine ■ Guanine ■ Cytosine ■ Thymine

DNA structure ● Difference between eukaryotic and prokaryotic ● Four nucleotide ● Complementary Base pairing → result of hydrogen bonds ○ Adenine → thymine ○ Guanine → cytosine ○ Always a double ring structure ● Structure explanation

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Always linked in the same way Always a sugar phosphate sugar phosphate backbone ■ Covalent bond → strong bond 3 prime end ■ 3 carbon that is not attached to another nucleotide 5 prime end ■ Phosphate group on #5 carbon that is not attached to another nucleotide ■ Always start with 5, build on the 3 end Has directionality Nitrogenous bases hang off to the side

■ Double helix ○ 2 backbones next to each other after being twisted into shape

○ Backbones will be antiparallel → think about the interstate ○ 3 prime to 5 prime up, 3 prime to 5 prime down ● Nitrogenous bases are hydrogen bonding down the middle → weak bonds holding backbones together ● Center structure is then twisted into a helix Adenosine Triphosphate ● Not only a component of nucleic acids, but also important in cellular energetics ●

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Comes in the form of ATP

Adenosine nucleotide ○ Adenine as base ○ Ribose as sugar ○ Instead of one phosphate group that has 3 → all nucleotides come in triphosphate forms ○ Release energy by cleaving off terminal phosphate group → ○ Generates adenosine diphosphate → ○ Cleave off second phosphate to release more energy → ○ Generates adenosine monophosphate → ○ The groups can be added back on to put energy back if needed

Online quiz 7 (oct 6) 1. In the accompanying image, a nucleotide is indicated by the letter (B)

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a. 2. Which of these is the difference between a DNA...