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BI-121 (Foundations Of Cellular/Molecular biology) > Exam III Study Guide > Flashcards

Exam III Study Guide Flashcards

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1
Q

Know the basic structure of ATP and its role as the energy currency of ALL cells

A

Adenosine TriPhosphate (ATP) Consists of three phosphate groups, ribose, and adenine

  • ATP contains energy in its chemical bonds, and it is the energy currency for all cells!
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2
Q

Know and compare Chemotrophs (auto traps vs heterotrophs) and Phototrophs (autotrophs vs heterotrophs).

A

Chemotrophs: Get their energy from Chemical Compounds

Phototrophs: Get their Energy from Sunlight

Autotroph: Get their Carbon from CO2

Heterotrophs: Get their Carbon from organic compounds

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3
Q

Describe and compare the metabolic processes of catabolism an anabolism.

A

Catabolism: Breakdown of molecules into smaller units to Produce ATP

Anabolism: Building of molecules from smaller units; Requires ATP Energy

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4
Q

Know the types of work that cells need to carry out.

A

Work of a Cell:

1) Synthesizing DNA/RNA/Proteins
2) Moving Vesicles
3) Pumping Substances across Membranes

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5
Q

Know and compare kinetic and potential energy

A

Kinetic Energy: Energy of Motion

Potential Energy: Stored energy, which can potentially be used to do work
* (Chemical Energy is a form of Potential Energy

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6
Q

Describe chemical energy

A

Chemical Energy: Energy stored within the bonds of a molecule. When an energy is broken, it releases energy

  • The inverse is also true — it takes energy to form bonds!
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7
Q

Know where chemical energy is stored within ATP

A

Within ATP, the Majority of ATP is stored in the Phosphate Groups!

  • The rest of the molecule is just Carbons, Nitrogen’s, and Hydrogens… Which aren’t very electronegative in comparison.
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8
Q

Define an open system in the context of thermodynamics

A

Open System: Energy and Matter can be transferred between the system and its surroundings

Example: Organisms are open systems: I can eat food, and absorb chemical energy — and my body can release thermal energy back into the atmosphere

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9
Q

Describe and compare the first and second laws of thermodynamics

A

First Law of Thermodynamics: Energy is neither creates nor destroyed — it transforms from one form to another

Second Law of Thermodynamics: There is a loss of energy available to do work when energy is transformed

  • Less Energy will be available after transforming
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10
Q

Define Gibbs Free Energy and describe its relationship to endergonic and exergonic reactions

A

Gibbs Free Energy: The amount of energy available in a system to “do work”

  • Endergonic Reaction: Products have more free energy than reactants; So Gibbs Free Energy is Positive
  • Exergonic Reaction: Products have less free energy than reactants; So Gibbs Free Energy is Negative!
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11
Q

Describe and compare endergonic and exergonic reactions

A

Endergonic: Starting Reactants have less energy than the Products (Energy is usually added to a reaction like this)

Exergonic: Starting Reactants have more energy than the products (Energy is lost in this reaction as products are formed, like the production of heat).

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12
Q

Know the definition of Gibbs free energy and the equation for calculating ΔG

A

ΔG= ΔH-T*ΔS

(G): Gibbs Free Energy
(H): Enthalpy, total energy available
(S): Entropy: Degree of Disorder
(T): Temperature: Absolute temperature in Kelvin, influences the movement of molecules and adds to the degree of disorder

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13
Q

Describe the relationship between Gibbs free energy and catabolism/anabolism.

A

Catabolic Reactions (Break one thing into many small parts): Products have less chemical energy than reactants, more disordered, yielding a negative ΔG

Anabolic Reactions (Building a large thing from small parts): The Products have more chemical energy than the reactants (Yielding a Positive ΔG).

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14
Q

Know the process of ATP hydrolysis

A

Adenosine TriPhosphate + Water —> Adenosine Diphosphate + Phosphate

    -ΔG= -ΔH - T*ΔS

    -ΔG: Exergonic Reaction
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15
Q

Describe the coupling of endergonic and exergonic reactions

A

Coupling of Endergonic and Exergonic Reactions allow for the Energy Lost in one reaction (Exergonic Reactions) to fuel the Activation Energy required for an Endergonic Reaction (Products have Greater Energy than Reactants).

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16
Q

Define the activation energy of a reaction and describe the role of enzymes

A

Activation Energy: The minimum input of energy required for a reaction to proceed

Role of Enzymes in Reactions: Reduces the Activation Energy Requirements (making it easier/faster to proceed).

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17
Q

Describe the active site of an enzyme (including its formation and interaction with substrate molecules)

A

Active Site: Region of an enzyme that binds the substrate and converts it to the product.

  • Interactions (between Substrate and Active Site) are typically Non-covalent, and help to stabilize the transition state; resulting in a decrease of activation energy.
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18
Q

Describe and compare competitive inhibition, non-competitive inhibition, and allosteric activation

A

Inhibitors: Decreases the activity of enzymes

Competitive Inhibition: The Enzyme binds either its substrate or its inhibitor

Non-Competitive Inhibition: The binding sites of the substrate and inhibitor are different, allowing for the Enzyme to bind to both.

Allosteric Activation: Positive effector binds to an enzyme, shaping its active site to one that is complementary to the substrate.

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19
Q

Describe positive and negative feedback

A

Positive Feedback: A positive feedback loop occurs in nature when the product of a reaction leads to an increase in that reaction. If we look at a system in homeostasis, a positive feedback loop moves a system further away from the target of equilibrium. It does this by amplifying the effects of a product or event and occurs when something needs to happen quickly.

Negative Feedback: A negative feedback loop occurs in biology when the product of a reaction leads to a decrease in that reaction. In this way, a negative feedback loop brings a system closer to a target of stability or homeostasis. Negative feedback loops are responsible for the stabilization of a system, and ensure the maintenance of a steady, stable state. The response of the regulating mechanism is opposite to the output of the event.

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20
Q

Know the definition and objective of cellular respiration

A

Cellular Respiration: The Process in which sugars (glucose) are converted into usable energy (ATP)

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21
Q

Know and describe the four stages of cellular respiration, including the order in which they occur relative to one another

A

The Four Stages of Respiration (in order) Are:

1) Glycolysis (Cytoplasm): Glucose is partially broken down, energy is released (Proteins and Lipids may also be broken down by different pathways.

2) Acetyl-CoA synthesis (Mitochondria): Pyruvate, produced in Glycolysis, is converted into Acetyl-CoA and CO2

3) Citric Acid Cycle (Mitochondria): Acetyl-CoA is broken down releasing CO2 energy, and electron carriers

4) Oxidative Phosphorylation (Mitochondria): Electron carriers from stages 1-3 release high-energy electrons to the electron transport chain, producing ATP

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22
Q

Describe oxidation-reduction reactions (including oxidizing agent, reducing agent, oxidized product, reduced product)

A

Oxidaition: Loss of Electrons (What is getting Oxidized, Making it the Reducing agent of the reaction).
Reduction: Gain of Electrons (What is getting Reduced, Making it the Oxidizing agent of the reaction).

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23
Q

Describe the breakdown of glucose relative to an oxidation-reduction reaction

Glucose —-> CO2 and H20

A

Glucose is broken down into Co2 and H20.

In this reaction, Glucose is the Electron donor (getting oxidized) —> Thus, it is considered to be the Reducing Agent.

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24
Q

Describe the process of carbohydrate catabolism

A

Chemical Energy is stored in bonds. The Chemical Energy of Glucose is transferred to the chemical bonds of ATP and Electron carriers as Glucose goes through Catabolism (broken down into smaller parts).

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25
Q

Define, describe, and compare the electron carriers NAD+ and FAD

A

Electron Carriers: Can accept electrons to become Reduced. Once it is Reduced, it can be used to Synthesize ATP

NAD+: Has Nitrogen and 3 rings
FAD: Has Fluorine and 3 rings.

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26
Q

Describe the process of substrate-level phosphorylation

A

Phosphorylation: Organic Molecule transfers one of their phosphate groups to ADP, Producing ATP

  • Substrate-Level Phosphorylation is used to generate all of the ATP during the stages of Glycolysis and the Citric Acid Cycle.
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27
Q

•Define glycolysis (and the impact of oxygen on this stage of respiration, is it anerobic or aerobic)

A

Process of Glycolysis is to take Glucose and refine it into Pyruvate.
* Process is anaerobic: Oxygen is not consumed
*2 Pyruvate molecules are produced for each glucose molecule used

28
Q

Know the 3 phases of glycolysis and the amounts of ATP, NADH, and pyruvate produced per glucose molecule by the end of glycolysis

A

Phase I: Preperatory Phase (Consumes 2 ATP)
* This Phase traps the molecule in the cell, and destabilizes it in preparation for Phase II
Phase II: Cleavage Phase (Refines Fructose-1,6-Biphosphate into Glyceraldehyde 3-Phosphate
* Two Molecules of Glyceraldehyde-3-Phosphate are produced
Phase III: Payoff Phase (Produces 4 ATP and 2 NADH)
* During this phase: 2 Pyruvate are formed, 2 Molecules of NADH are made, 4 Molecules of ATP are produced!

Per Glucose:
4 ATP are produced, Net Yield of 2
2 Molecules of NADH are produced
2 Pyruvate are produced

29
Q

For the 3 phases of glycolysis, you will be expected to know the reactants and products for those reactions that (1) require ATP to proceed (2) produce ATP and (3) reduce NAD+ to NADH

A

• Step 1: Glucose + ATP —> Glucose-6-Phosphate + ADP
◦ The Phosphate group on the glucose will trap it within the Cytoplasm

• Step 3: Fructose-6-Phosphate + ATP —> Fructose-1,6-biphosphate + ADP
◦ Purpose was to Destabilize the Sugar

• Step 4: Fructose-1,6-biphosphate + ADP —> Glyceraldehyde 3-Phosphate + Dihydroxyacetone Phosphate
◦ Main Cleavage Reaction
‣ Glyceraldehyde 3-Phosphate is directly ready for Phase 3, but Dihydroxyacetone cannot be used in Phase 3… So we must refine Dihydroxyacetone first!

• Step 6: (2x) Glyceraldehyde 3-Phosphate + (2) Phosphate+ (2) Nad+ —> (2) 1,3-Biphosphoglycerate + (2) NADH
◦ Starting to Produce NADH
‣ NAD^+ Gains electrons, which means it gets reduced (NAD^+ is also the oxidizing agent).
‣ Glyceraldehyde will be losing electrons, (getting oxidized) making it the Reducing Agent

• Step 7: (2) 1,3-Biphosphoglycerate + (2) ADP —> (2) ATP + (2) 3-Phosphoglycerate
◦ Substrate-Level Phosphorylation

• Step 10: (2) Phosphoenolypyruvate + (2) ADP —>(2) ATP + Pyruvate

30
Q

Know the basic structure of a mitochondria

A

Composed of an Inner and Outer membrane.

Inter membrane Space: Between the two membranes

Mitochondrial Matrix: Inside the inner membrane

31
Q

Know the Acetyl CoA Synthesis reaction; including where it takes place in the cell, its requirement for oxygen, the basic components of the reaction and its catalysis by the Pyruvate Dehydrogenase Complex

A

In the presence of oxygen, Pyruvate is transported inside of the mitochondrial matrix. Then, Pyruvate is converted to Acetyl CoA

  • Reaction also releases CO2
  • Catalyzed by a group of enzymes called: Pyruvate Dehydrogenase Complex
32
Q

For the Citric Acid Cycle (CAC), you will be expected to know
–the reactants and products of those reactions that (i) produce ATP, (ii) reduce NAD+ to NADH and FAD to FADH2, (iii) generate CO2
– the cellular location of the CAC
– the compound that is regenerated by the end of the cycle to allow it to proceed again

A
  • CAC takes place inside of the Mitochondrial Matrix
  • Oxaloacetate is regenerated at the end

Step 4: Alpha-Ketoglutarate loses a molecule of CO2 and is oxidized, reducing NAD+ to NADH.
• The remaining molecule is attatched to coenzyme A by an unstable bond to form Succinyl CoA

Step 5: CoA is displaced by a phosphate group, which is transferred to GDP, forming GTP: A molecule with functions similar to ATP
• GTP is used to Generate ATP
• The molecule, Succinate, is formed.

Step 6:Two hydrogens are transferred from Succinate to Fad, forming FADH2 and oxidizing Succinate to form Fumarate

Step 8: Malate is oxidized, reducing NAD+ to NADH and regenerating Oxaloacetate

33
Q

Know how much ATP, NADH and FADH2 is produced per molecule of glucose during the CAC (as well as per molecule of Acetyl CoA that enters into the cycle)

A

Per Molecule of Glucose Used in Citric-Acid-Cycle (Kreb’s Cycle) produces:

  • (2) ATP’s
  • (6) NADH
  • (2) FADH2

Remember - 1 glucose makes 2 Pyruvate —> 2 Acetyl-CoA.

So every Acetyl CoA makes:
1. ATP
2. 3 NADH
3. 1 FADH2

34
Q

Know the flow of electrons during respiration

A

Electrons go downhill: Glucose —> NADH —> Electron transport Chain —> Oxygen

35
Q

Describe the role of the electron transport chain in controlling the release of energy during oxidative phosphorylation

A

The electron transport chain passes electrons in a series of steps instead of one explosive reaction

36
Q

Know the location of the electron transport chain and the multi-protein complexes that make up that chain

A

The electron transport chain is in the inner membrane of the Mitochondrion
* It’s composed of Multiprotein Complexes (1-4).

37
Q

Know how the free energy of electrons change as they move through the electron transport chain and combine with the final electron acceptor, oxygen, to form water.

A

Electrons drop in free energy as they go down the chain —> Until finally passed to O2, reducing it into H2O

38
Q

Know the complexes to which NADH and FADH2 Donate their electrons and describe the path these electrons take as they travel through the electron transport chain

A

NADH donates an electron to Complex I; FADH2 Donates two electrons to Complex II. Both complex 1 & 2 get reduced to CoQH2; which transfers the electrons to Complex III.

Complex III Transfers electrons to Cytochrome C

This gets reduced, and interacts with Complex #4. —> Which reduces oxygen and produces water

39
Q

Describe how oxidation and reduction relates to the movement of electrons through the electron transport chain

A

Oxidation: Losing of electrons
Reduction: gaining of Electrons

OIL-RIG
Oxidation-is-losing & Reducing-is-Gaining. [Electrons]

40
Q

Describe the role of protons in the electron transport chain including the region where they accumulate within the mitochondria

A

Protons in the inter-membrane space diffuse down their electrical concentration gradients through ATP Synthase into the mitochondrial matrix; this gives power to the ATP Synthase Enzyme and catalyzes the Production of ATP.

41
Q

Describe the Relationship between proton concentrations within the Mitochondria and ATP Synthase

A

Movement of protons is coupled with ATP synthase. Because F1 subunit uses rotational energy (provided by proton concentration) to catalyze the Synthesis of ATP.

42
Q

Describe how the movement of protons through ATP Synthase generates ATP

A

Proton flow through F0 causes it to rotate: Converts proton gradient energy into mechanical rotation energy — > Causes a conformational change in ATP Synthase that allows it to Catalyze the synthesis of ATP.

43
Q

Describe and Compare the processes of lactic Acid and Ethanol Fermentation; Including the circumstances during which they occur.

Also - the reactions that are carried out in order to make them happen, and the amount of energy they generate

A

Lactic Acid: This type of Fermentation produces 2 ATP, and it occurs in the absence of oxygen for animals and bacteria.

Ethanol Fermentation: Occurs in Plants and Fungi with the Absence of Oxygen; this reaction also produces 2 ATP.

44
Q

Know How Excess glucose is stored in animal and plant cells. Know the process stored glucose (glycogen) undergoes in order to participate in Glycolysis.

A

In animals, excess glucose is stored in Muscle and liver cells. This allows for the muscles to have the ATP needed to contract. Glycogen in the liver kinda just chills, and waits until it is needed.

In Plants, excess glucose is stored as Starch.

In order to be used in Glycolysis, glycogen is cleaved - and little glucose molecules are broken off from the ends of the chain. (Originally as Glucose-1-Phosphate). Then, they are converted into glucose 6-phosphate and then can be used in Glycolysis.

45
Q

Know the Contribution of other sugars to Glycolysis

A

Sucrose, Maltose, Lactose, Galactose, Fructose, and Mannose can also contribute to Glycolysis.

Many disaccharides and polysaccharides can be used in Glycolysis, not just Glucose!

46
Q

Describe the Process of Beta-Oxidation and its role in harvesting energy from lipids

A

Beta Oxidation breaks down Fatty acid chains, by removing 2-carbon units from the ends. This results in the production of NADH, FADH2, and Acetyl-CoA.

47
Q

Describe how ATP levels regulate Cellular Respiration

A

ATP levels within the cell regulate the rate at which the cell respirates.

Low Levels — Cell will activate pathways that lead to ATP Synthesis

High Levels — Cell stops/inhibits pathways that lead to ATP Synthesis

48
Q

Describe how the Enzyme Phosphofructokinase-1 responds to varying ATP concentrations in the cell.

A

When ATP levels are low, PFK-1 is activated, allowing glycolysis to continue

When ATP levels are high, PFK-1 is inhibited/de-activated, which slows down Glycolysis.

49
Q

Net Gain for Every Molecule of Glucose That Enters Glycolysis:

A

2 ATP
2 NADH
2 Pyruvate

50
Q

The Citric Acid Cycle (Krebs Cycle) completes the Breakdown of Pyruvate to Co2. But what does it generate per molecule of Glucose

A

Well, the Cycle generates

2 ATP
6 NADH
2 FADH2

For every molecule of Glucose that comes into the cycle!

51
Q

Where is the Electron Transport Chain in Oxidative Phosphorylation

A

Inside the Inner Membrane of the Mitochondria

Between the Mitochondrial Matrix and the Inter-Membrane Space

52
Q

Define Photosynthesis:

A

The biochemical process of building carbohydrates form Sunlight, Carbon Dioxide, and Water

53
Q

Describe the structure of chloroplasts and their role in Photosynthesis

A

Structure of Chloroplasts: 3 membranes: Outer, Inner, and Thylakoid Membrane

Thylakoid membranes for Grana (Flattened sacs that are grouped into stacks)
- Within each Grana is the lumen; the area outside of the Grana is the Stroma.

54
Q

Know the Photosynthesis reaction, including components that are reduced/oxidized

A

6 CO2 + 12 H20 + Light = Glucose + 6 O2 + 6 H20

  • CO2 Gets reduced
  • H20 Gets oxidized
55
Q

Know the main type of electron carrier in Photosynthesis

A

Main Electron carrier in photosynthesis is NADP+/NADPH

56
Q

Know the two phases of Photosynthesis and describe what happens during each phase

A

Phase 1: Light Reactions (Occurs in Thylakoid Membrane)
* Produces ATP and NADPH to power Calvin Cycle
Phase II: Calvin Cycle (Occurs in Stroma)
* Formation of Sugar from CO2 using ATP and NADPH
* it takes 3 CO2 to produce 1 G3P and sustain the entire cycle

57
Q

Know and Describe the three phases of the Calvin Cycle, including the intermediates that we covered in class

A

Phase 1: Carbon Fixation
* CO2 binds with RUBP to make a 6-carbon-sugar, then it gets split into TWO 3-carbon-sugars.

Phase 2: Reduction
* Each 3-phosphoglycerate receives a Phosphate from ATP to become 1,3-biphosphoglycerate.
* Then, each sugar loses a phosphate group and is reduced to G3P
* Phase 1-2 repeats until there is 6 G3P’s available

Phase 3: RuBP Production
*One G3P is taken as the overall product of the Calvin cycle, the last 5 get combined back into RuBP so that the cycle can continue

Summary: In order to synthesize 1 G3P from 3 CO2, the cycle needs 9 ATP and 6 NADPH

58
Q

Describe the Role of Starch in Plant Cells

A

Start provides photosynthetic cells with a source of carbohydrates that can be used in the absence of sunlight.

59
Q

Describe the role of the lights reactions in photosynthesis

A

Light Reactions convert Solar Energy into the Chemical Energy of ATP and NADPH

60
Q

Describe the basic properties of lights and how wavelength affects energy

A

Light is a form of electromagnetic energy
Light travels in Rhythmic Waves

Wavelength is the distance between crests of waves

How does wavelength affect energy? Well, light particles with the smallest wavelengths have the highest energy.

61
Q

Define the electromagnetic spectrum and know the range that drives photosynthesis

A

Electromagnetic spectrum is the entire range of electromagnetic energy, or radiation

Visible light consists of the wavelengths that are used to drive photosynthesis. Ranging from 380-750nm

62
Q

Know the main photosynthetic pigment in plants

A

Chlorophyll “A” is the main photosynthetic pigment!

63
Q

Know the accessory pigments (in photosynthesis) and describe their functions

A

Chlorophyll B: Acessory pigment that broadens the spectrum of light used for photosynthesis

Carotenoids: Accessory pigments that absorb excessive light that would Damage Chlorophyll

64
Q

Describe how Chlorophyll is excited by light

A

When pigments inside of Chlorophyll absorbs light, it goes from a stable ground state to an unstable excited state.

  • When it is excited, it releases heat and another photon, before returning to its ground state
  • release of this second photon activates other Chlorophyll Molecules
65
Q

Describe the structure and function of a photosystem

A

Photosystems consist of reaction-center complexes surrounded by light-harvesting complexes

  • Photosystems provide enough energy to pull electrons from water and then use them to Reduce NADP+
  • The photosynthetic electron tranpsort chain connects Photosystem I and Photosystem II
66
Q

Know the two types of Photosystems involved in Photosynthesis, the wavelength of light they optimally absorb, and the name of their respective reaction center Chlrophyll A molecules.

A

PS1: Absorbs light best at 700nm
* The reaction center Chlroophyll A of PS1 is called “P700”

PS2: Functions first and is best at absorbing a wavelength of 680nm
*The Reaction-center Chlorophyll A of PSII is called “P680”

67
Q

Describe the flow of electrons within and between Photosystems II and I; including any enzymes that are represented, where and how ATP and NADPH production is occurring, and where water is being split

A

PS #2 gets excited by a new photon, Chlorophyll A pass around the photon until it reaches P680. Then P680 gets excited, and climbs up to the excited state, Then, this primary electron acceptor splits a water molecule — and then enters the electron transport chain.

The electron transport chain is made up of the electron carriers: Plastoquinone (Pq), a cytochrome complex (ATP is made here), and Plastyocyanin (Pc) and then reaching PS1.

Photoexcited electrons are passed in a series of redox reactions from the Primary electron acceptor of PSI down a second Electron Transport Chain through the protein Ferredoxin (Fd).

The enzyme NADP+ reductive catalyzes the transfer of electrons from Fd to NADP+, which is reduced to NADPH (NADPH is produced in the Stroma, and ATP is also produced into the Stroma).

Both ATP and NAPDH are produced in the Stroma, so that they can go directly into the Calvin Cycle

BI-121 (Foundations Of Cellular/Molecular biology) (4 decks)

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