Exam 2 huge study

1. What is metabolism? Describe what a metabolic pathway is.

• Metabolism: The total of all chemical reactions that occur within a cell or organism.

• Metabolic pathway: A series of chemical reactions where the product of one reaction becomes the reactant for the next reaction.

2. Compare and contrast anabolic pathways and catabolic pathways.

• Anabolic pathways: Build larger molecules from smaller molecules; they require energy.

• Catabolic pathways: Break larger molecules into smaller molecules; they release energy.

• Both are parts of metabolism.

3. What are the two forms of energy? What is an example of each type of energy?

• Kinetic energy: Energy of motion. Example: a moving object.

• Potential energy: Stored energy. Example: chemical energy stored in ATP or glucose.

4. What are the two laws of thermodynamics?

• First Law: Energy cannot be created or destroyed, only transferred or transformed.

• Second Law: Every energy transfer or transformation increases the entropy (disorder) of the universe.

5. What are the characteristics of reactions with a (+) and (-) change in free energy (ΔG)?

• Positive ΔG: Requires an input of energy and is endergonic. It is not spontaneous.

• Negative ΔG: Releases free energy and is exergonic. It can occur spontaneously.

6. What are the two equations for determining ΔG?

1. ΔG = ΔH − TΔS

2. ΔG = G(products) − G(reactants)

7. What is ATP?
ATP (adenosine triphosphate) is the main energy-carrying molecule used by cells. It stores and transfers energy for cellular processes.

8. How is ATP made?
ATP is made by adding a phosphate group to ADP using energy:

ADP + Pi + energy → ATP

9. How is ATP hydrolysis used?
ATP hydrolysis breaks ATP into ADP and phosphate, releasing free energy. Cells use this energy to power processes such as active transport, movement, and chemical reactions.

10. What is activation energy and why is it important?
Activation energy (Ea) is the minimum amount of energy required to start a chemical reaction. It is important because reactants must reach this energy level before the reaction can occur.

11. What is a transition state?
The transition state is the unstable, high-energy state that molecules temporarily reach during a chemical reaction.

12. Using the free energy diagram, indicate the transition state, ΔG, and activation energy.
On a typical free-energy diagram:

• Transition state: The highest point on the curve.

• Activation energy: The energy difference between the reactants and the highest point.

• ΔG: The energy difference between the reactants and products.

  • Products lower than reactants → negative ΔG.

  • Products higher than reactants → positive ΔG.

Enzymes

13. What are enzymes? What do they do to help reactions happen?
Enzymes are biological catalysts, usually proteins. They speed up chemical reactions by lowering the activation energy without being consumed by the reaction. Ch 8 Study Guide

14. Use the free energy diagram above to sketch what the reaction would look like if an enzyme were used to facilitate this reaction.
The enzyme would make the activation-energy peak lower, but the starting and ending energy levels would stay the same. The ΔG of the reaction does not change.

15. What are the two different types of sites on an enzyme?

• Active site: Where the substrate binds and the chemical reaction occurs.

• Allosteric site: A separate location where molecules can bind and change the enzyme's activity.

16. What factors affect an enzyme’s ability to function?
Important factors include:

• Temperature

• pH

• Substrate concentration

• Enzyme concentration

• Inhibitors

• Activators

• Availability of necessary cofactors/coenzymes

17. What is “induced fit”?
Induced fit is when an enzyme changes its shape slightly after the substrate binds, allowing the enzyme and substrate to fit together more closely and making the reaction easier.

18. What is the difference between competitive inhibition and noncompetitive/allosteric inhibition?

• Competitive inhibition: The inhibitor binds to the active site, competing with the substrate.

• Noncompetitive/allosteric inhibition: The inhibitor binds to an allosteric site, changing the enzyme's shape and reducing its ability to function.

19. Explain how activators and inhibitors work to activate or deactivate an enzyme.

• Activators bind to an enzyme and help it maintain or achieve its active shape, increasing enzyme activity.

• Inhibitors decrease enzyme activity by interfering with substrate binding or changing the enzyme's shape.

20. What is allosteric regulation?
Allosteric regulation is the regulation of an enzyme by molecules binding to a site other than the active site. This binding can either activate or inhibit the enzyme.

Chapter 9 — Cellular Respiration

1. What are three catabolic pathways that release stored energy by breaking down organic molecules? How are these pathways different?

• Glycolysis: Breaks glucose into pyruvate.

• Citric acid cycle (Krebs cycle): Further breaks down the products of glucose oxidation and produces electron carriers.

• Fermentation: Allows glycolysis to continue when oxygen is unavailable by regenerating NAD⁺.

• They differ in what molecules they break down, where they occur, and whether oxygen is required.

2. What are the reactants and products of cellular respiration? Which reactant gets reduced and which gets oxidized?

• Reactants: Glucose + O₂

• Products: CO₂ + H₂O + ATP

• Glucose is oxidized → CO₂

• O₂ is reduced → H₂O

3. What can be used as “fuel” for cellular respiration?

• Carbohydrates

• Fats

• Proteins

4. What is a redox reaction? What are oxidation and reduction?

• Redox reaction: A reaction involving the transfer of electrons.

• Oxidation: Loss of electrons.

• Reduction: Gain of electrons.

• Remember: OIL RIG → Oxidation Is Loss, Reduction Is Gain.

5. What is an oxidizing agent? What is a reducing agent?

• Oxidizing agent: Accepts electrons and becomes reduced.

• Reducing agent: Donates electrons and becomes oxidized.

6. What are the two electron acceptors in aerobic respiration?

• NAD⁺

• FAD

• They accept electrons and hydrogen to become NADH and FADH₂.

7. What are the three stages of aerobic respiration?

1. Glycolysis

2. Citric acid cycle

3. Oxidative phosphorylation

Pyruvate oxidation occurs between glycolysis and the citric acid cycle. Ch 9

8. Describe the phases of cellular respiration.

9. What is substrate-level phosphorylation?
It is the direct production of ATP by transferring a phosphate group from a substrate to ADP.

10. What does glycolysis mean?
Glycolysis = “sugar splitting.” It is the process of breaking one glucose molecule into two pyruvate molecules.

11. What are the two phases of glycolysis? What do we invest/gain from each?

• Energy investment phase: Uses 2 ATP to activate glucose.

• Energy payoff phase: Produces 4 ATP and 2 NADH.

• Net gain: 2 ATP + 2 NADH + 2 pyruvate.

12. Under what condition does pyruvate enter the mitochondria during cellular respiration?
When oxygen is available and the cell is performing aerobic respiration, pyruvate can enter the mitochondrion for further oxidation.

13. What is made as a result of pyruvate oxidation? Why is this important?
Each pyruvate produces:

• 1 acetyl-CoA

• 1 NADH

• 1 CO₂

Since one glucose produces two pyruvate, per glucose:

• 2 acetyl-CoA

• 2 NADH

• 2 CO₂

This is important because acetyl-CoA enters the citric acid cycle.

14. What do we get from 1 turn of the citric acid cycle? What do we get from 2 turns?
1 turn:

• 1 ATP

• 3 NADH

• 1 FADH₂

• 2 CO₂

2 turns (per glucose):

• 2 ATP

• 6 NADH

• 2 FADH₂

• 4 CO₂

15. Oxidative phosphorylation consists of two parts. What are they?

1. Electron transport chain (ETC)

2. Chemiosmosis

16. What is the electron transport chain?
The ETC is a series of protein complexes in the inner mitochondrial membrane. Electrons from NADH and FADH₂ move through the chain, releasing energy that is used to pump H⁺ ions across the membrane.

Its purpose is to create a proton gradient that can be used to make ATP. Ch 9

17. What is chemiosmosis?
Chemiosmosis is the process where H⁺ ions flow down their concentration gradient through ATP synthase.

• Mechanism: H⁺ flows through ATP synthase.

• Enzyme: ATP synthase.

• End result: ADP + Pi → ATP.

18. Describe the flow of energy during cellular respiration.
Energy flows approximately like this:

Glucose → NADH/FADH₂ → Electron Transport Chain → H⁺ gradient → ATP

Glucose's chemical energy is gradually transferred to electron carriers and ultimately used to make ATP.

19. How does anaerobic respiration differ from aerobic/cellular respiration?

• Aerobic respiration: Uses oxygen as the final electron acceptor and produces much more ATP.

• Anaerobic respiration: Does not use oxygen as the final electron acceptor and generally produces less ATP.

20. How is fermentation similar and different from anaerobic respiration?
Similar:

• Both occur without oxygen.

• Both allow cells to continue producing ATP through glycolysis.

Different:

• Fermentation uses an organic molecule as the final electron acceptor.

• Anaerobic respiration uses another inorganic molecule instead of oxygen as the final electron acceptor.

21. What does fermentation consist of?
Fermentation consists of:

1. Glycolysis

2. A process that converts NADH back into NAD⁺

This allows glycolysis to continue producing ATP when oxygen is unavailable.

22. What are the two common types of fermentation? What are their final electron acceptors and products?

• Lactic acid fermentation

  • Final electron acceptor: Pyruvate

  • Product: Lactate

• Alcohol fermentation

  • Final electron acceptor: Acetaldehyde

  • Products: Ethanol + CO₂

23. How do cells regulate/control catabolism?
Cells regulate catabolism mainly through feedback inhibition and enzyme regulation. When enough ATP or other products are available, enzymes involved in catabolic pathways can be inhibited. When energy is needed, these pathways become more active. Ch 9

Chapter 10 Study Guide: Photosynthesis

1. What is photosynthesis and where does it occur?

Photosynthesis is the process of converting light energy into chemical energy stored in sugars.

• In plants, it occurs in the chloroplasts.

• It uses light energy, carbon dioxide, and water to produce sugars and oxygen.

2. What types of organisms does photosynthesis occur in?

• Plants

• Algae

• Photosynthetic bacteria, including cyanobacteria

3. What are autotrophs and heterotrophs?

• Autotrophs: Organisms that produce their own organic food using light or chemical energy. Example: plants.

• Heterotrophs: Organisms that obtain energy and nutrients by consuming other organisms or organic matter. Example: animals.

4. What are the major sites of photosynthesis?

In plants, photosynthesis primarily occurs in the leaves, especially in the mesophyll cells. Within those cells, photosynthesis occurs in the chloroplasts.

5. Describe the structure of chloroplasts and mesophyll tissue.

• Chloroplast: An organelle surrounded by a double membrane.

• Thylakoids: Flattened membrane sacs where the light reactions occur.

• Grana: Stacks of thylakoids.

• Stroma: Fluid surrounding the thylakoids where the Calvin cycle occurs.

• Mesophyll tissue: Internal leaf tissue containing many chloroplasts.

  • Palisade mesophyll: Tightly packed cells that absorb much of the incoming light.

  • Spongy mesophyll: Loosely arranged cells with air spaces that facilitate gas exchange.

6. What are the reactants and products of photosynthesis?

The overall equation is:

\[ 6CO_2+6H_2O+\text{light energy} \rightarrow C_6H_{12}O_6+6O_2 \]

• Reactants: Carbon dioxide, water, and light energy.

• Products: Glucose (sugar) and oxygen.

The oxygen released comes from water, not carbon dioxide.

CO₂ and Water are limiting, so the photosynthesis rate is medium

Light intensity

Low levelMedium levelHigh level

Carbon dioxide (CO₂) availability

Low levelMedium levelHigh level

Water availability

Low levelMedium levelHigh level

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7. What are the two stages of photosynthesis?

Stage 1: Light reactions

Location: Thylakoid membranes

• Require light.

• Split water, releasing oxygen.

• Produce ATP and NADPH.

• Purpose: Convert light energy into chemical energy.

Stage 2: Calvin cycle

Location: Stroma

• Does not directly require light.

• Uses CO₂, ATP, and NADPH.

• Produces G3P, a sugar molecule.

• Purpose: Incorporate carbon dioxide into organic molecules.

8. Describe the nature of sunlight.

• Sunlight is electromagnetic radiation that travels in waves and behaves as particles called photons.

• Each photon carries energy.

• The amount of energy depends on its wavelength: shorter wavelengths have more energy, while longer wavelengths have less energy.

• Photosynthetic pigments absorb certain wavelengths of light.

9. Be able to read and interpret absorption spectra.

An absorption spectrum shows how much light a pigment absorbs at different wavelengths.

• The x-axis represents wavelength, usually in nanometers (nm).

• The y-axis represents the amount of light absorbed.

• High peaks indicate wavelengths absorbed strongly.

• Low points indicate wavelengths absorbed poorly.

For chlorophyll:

• Blue-violet light: Strong absorption.

• Red light: Strong absorption.

• Green light: Weak absorption, so much of it is reflected or transmitted.

Remember: An absorption spectrum measures light absorbed, not light reflected.

10. What is the range of visible light?

Visible light is approximately 380–750 nm.

• Violet: shortest wavelengths

• Blue

• Green

• Yellow

• Orange

• Red: longest wavelengths

Some textbooks use a slightly different range, such as 400–700 nm.

11. What are pigments, how do they vary, and why are they important? Which pigments are involved?

Pigments are molecules that absorb particular wavelengths of light.

Different pigments have different molecular structures, allowing them to absorb different wavelengths.

Important photosynthetic pigments include:

• Chlorophyll a: The primary pigment involved in the reaction centers.

• Chlorophyll b: An accessory pigment that expands the range of light absorbed.

• Carotenoids: Accessory pigments that absorb blue and blue-green light and help protect against damage from excess light.

These pigments help organisms capture more of the available light energy.

12. What happens when a pigment absorbs a photon of light?

1. The pigment absorbs a photon.

2. An electron gains energy and moves to a higher energy level.

3. The excited electron's energy can be transferred to another pigment or the electron can be transferred to an electron acceptor.

4. This energy helps power the light reactions of photosynthesis.

13. What two things make up a photosystem? What are their features?

A photosystem consists of two major components:

• Light-harvesting complex (antenna complex): Contains pigment molecules that absorb photons and transfer excitation energy toward the reaction center.

• Reaction center: Contains a special pair of chlorophyll a molecules and a primary electron acceptor. The excited chlorophyll transfers an electron to the acceptor.

14. How many photosystems are involved in photosynthesis?

There are two photosystems in oxygen-producing photosynthesis:

• Photosystem II (PSII): Acts first in the linear electron flow pathway. It replaces lost electrons by splitting water.

• Photosystem I (PSI): Re-energizes electrons so they can ultimately help reduce NADP⁺ to NADPH.

Although named Photosystem II and Photosystem I, PSII functions before PSI in linear electron flow.

15. Understand linear electron flow.

Linear electron flow moves electrons from water through PSII and PSI to NADP⁺.

The sequence is:

1. PSII absorbs light, exciting electrons in its reaction center.

2. Water is split to replace the lost electrons, releasing O₂ and H⁺.

3. Electrons travel through an electron transport chain, helping establish a proton gradient.

4. PSI absorbs light and re-energizes the electrons.

5. Electrons are transferred to NADP⁺, producing NADPH.

Source of electrons: Water (H₂O).

Why is reaction-center chlorophyll special? Its position and molecular environment allow it to donate excited electrons to a primary electron acceptor.

Products of the light reactions:

• ATP: Supplies energy for the Calvin cycle.

• NADPH: Supplies high-energy electrons for the Calvin cycle.

• O₂: Released as a byproduct of water splitting.

16. Which photosystem is involved in cyclic electron flow? What is produced, and what is one benefit?

• Photosystem involved: Photosystem I (PSI).

• Main product: ATP.

• Electron flow: Electrons from PSI cycle back through an electron transport pathway and return to PSI.

• What it does not produce: NADPH or O₂.

Benefit: It provides additional ATP to help meet the Calvin cycle's energy requirements when linear electron flow does not supply enough ATP relative to NADPH.

17. Compare chemiosmosis in mitochondria and chloroplasts.

Similarity: Both use an electron transport chain to establish a proton gradient. H⁺ flows through ATP synthase, powering ATP production.

Difference: Mitochondria use energy from food-derived electrons, while chloroplasts use light energy to power electron flow.

18. What are the three phases of the Calvin cycle?

1

Carbon fixation

CO₂ is attached to RuBP, a five-carbon molecule. The unstable six-carbon intermediate splits into two molecules of 3-PGA.

2

Reduction

ATP and NADPH provide energy and electrons to convert 3-PGA into G3P, a three-carbon sugar.

3

Regeneration of RuBP

ATP is used to regenerate RuBP so the cycle can continue fixing more CO₂.

19. What is the end product of the Calvin cycle?

The direct sugar product is G3P (glyceraldehyde-3-phosphate).

• One net G3P requires 3 CO₂.

• Two net G3P molecules can be used to build one glucose molecule.

• G3P is also used to make other organic molecules.

20. What reaction occurs during carbon fixation? What enzyme catalyzes it?

• Reaction: CO₂ combines with RuBP, a five-carbon molecule, producing an unstable six-carbon intermediate that splits into two molecules of 3-PGA.

• Enzyme: RuBisCO (ribulose-1,5-bisphosphate carboxylase/oxygenase).

RuBisCO is the enzyme responsible for incorporating inorganic carbon dioxide into an organic molecule.

21. What is photorespiration?

Photorespiration occurs when RuBisCO binds to oxygen instead of carbon dioxide.

• It uses O₂ and RuBP.

• It releases CO₂.

• It consumes energy.

• It does not produce sugar, so it reduces the efficiency of photosynthesis.

Photorespiration is more likely under hot, dry conditions when plants close their stomata to conserve water, causing CO₂ levels inside the leaf to fall relative to O₂.