Chapter 3: Energy, Chemical Reactions, Enzymes, and Cellular Respiration

What is the definition of energy?

The capacity to do work. (Unlike matter, it has no mass and does not take up space).

What are the two major classes of energy?

Potential energy and kinetic energy.

What is potential energy?

The energy of position, or stored energy.

What is kinetic energy?

The energy of motion.

In a cell, a concentration gradient (like a high amount of Na⁺ outside the plasma membrane) represents what class of energy?

Potential energy. (When the ions move down their gradient into the cell, it converts to kinetic energy).

What is chemical energy?

A form of potential energy stored in a molecule's chemical bonds. It is the most important form of energy in the human body.

What three high-energy molecules function primarily in chemical energy storage in the human body?

1. Triglycerides (long-term storage)

2. Glucose (stored as glycogen)

3. ATP (stored in limited amounts, used immediately)

What is thermodynamics?

The study of energy transformations.

State the First Law of Thermodynamics.

Energy can neither be created nor destroyed—it can only be transformed or converted from one form to another.

State the Second Law of Thermodynamics.

Every time energy is transformed from one form to another, some of that energy is converted to heat (meaning conversion is never 100% efficient).

What is metabolism?

The collective term for all biochemical reactions in living organisms.

When does a chemical reaction occur?

When either the chemical bonds of molecular structures are broken and new ones formed, or electrons are transferred.

What is a chemical equation and what are its two components?

A summary of molecular changes in a reaction. Its components are reactants (substrates present before the reaction starts, written on the left) and products (substances formed by the reaction, written on the right).

Chemical reactions are classified based on what three criteria?

1. Changes in chemical structure

2. Changes in chemical energy

3. Whether the reaction is irreversible or reversible

What is a decomposition reaction?

A reaction where an initial large molecule is digested or broken down into smaller structures (AB → A + B).

What is the collective term for all decomposition reactions in the body?

Catabolism (or catabolic reactions).

What is a synthesis reaction?

A reaction that occurs when two or more atoms, ions, or molecules combine to form a larger chemical structure as existing bonds are broken and new bonds form (A + B → AB).

What is the collective term for all synthesis reactions in the body?

Anabolism (or anabolic reactions).

What is an exchange reaction?

A reaction in which atoms, molecules, ions, or electrons are exchanged between two chemical structures (AB + C → A + BC). It has both decomposition and synthesis components and is the most prevalent type of reaction in the body.

What is an oxidation-reduction (redox) reaction?

A specific type of exchange reaction that involves the movement of electrons from one chemical structure to another.

In a redox reaction, what is the difference between oxidation and reduction?

Oxidation is the loss of electrons (molecule becomes oxidized). Reduction is the gain of electrons (molecule becomes reduced/decreased in negative charge). (Mnemonic: LEO says GER)

What is the definition of reaction rate?

The measure of how quickly a chemical reaction takes place, determining the amount of product formed per unit of time.

What is activation energy (Eₐ)?

The amount of energy required to break existing chemical bonds for a chemical reaction to proceed.

What is a catalyst?

A substance that accelerates or promotes a chemical reaction without being consumed by it.

What are enzymes and what is their primary function?

Biologically active catalysts (mostly globular proteins) that facilitate chemical changes in the body by decreasing the activation energy (Eₐ) to increase the reaction rate.

Do enzymes cause reactions to happen that wouldn't normally occur?

No. They only facilitate chemical reactions that would already occur on their own; they just make them happen much faster.

What is the active site of an enzyme?

A unique, three-dimensional depressed or grooved region on the enzyme's surface that temporarily accommodates the specific substrate(s).

What is an enzyme-substrate complex?

The temporary structure formed when a substrate binds specifically to the active site of its matching enzyme.

Explain the Induced-Fit Model of enzyme function.

When a substrate enters the active site, it induces the enzyme to change its shape slightly for an even closer, tighter fit (like a hug), placing stress on the substrate's chemical bonds.

What are the 4 basic steps of enzyme catalysis?

1. Substrate enters active site.

2. Enzyme changes shape slightly (induced fit), stressing bonds.

3. Activation energy is lowered, bonds break/form, creating product.

4. Product is released, enzyme repeats process.

What is a cofactor?

A nonprotein "helper" structure (inorganic ion or organic molecule) required for the normal function of an enzyme.

What is the difference between an inorganic cofactor and an organic cofactor (coenzyme)?

Inorganic cofactors are attached to the enzyme (e.g., Zinc ion). Organic cofactors (coenzymes) are not permanently attached and are often vitamins or modified nucleotides (e.g., NAD⁺).

What suffix do the names of most enzymes end with?

-ase (usually added to the name of the substrate or the action it performs, like lactase or pyruvate dehydrogenase).

What do kinase enzymes do?

They belong to the transferase class and specifically transfer a phosphate group (usually from ATP) to another molecule.

What do dehydrogenase enzymes do?

They belong to the oxidoreductase class and participate in redox reactions by moving hydrogen from one molecule to another.

What does enzyme saturation mean?

It occurs when the substrate concentration is so high that all available enzyme active sites are constantly occupied, meaning the reaction rate cannot increase any further.

What is the optimum temperature for human enzymes, and what happens if it gets too high?

Around 37°C to 40°C (98.6°F to 104°F). Higher temperatures weaken intramolecular bonds, causing the enzyme to denature (permanently lose shape and function).

What is the optimum pH for most human enzymes, and what are the exceptions?

Most function best between pH 6 and 8. Exceptions include stomach enzymes like pepsin, which has an optimum pH between 2 and 4.

What is an enzyme inhibitor?

A substance that binds to an enzyme and turns it off, temporarily preventing it from catalyzing a reaction.

How does a competitive inhibitor work?

It physically resembles the substrate and competes to bind directly to the active site. (Its effects can be overcome by increasing substrate concentration).

How does a noncompetitive (allosteric) inhibitor work?

It binds to a separate allosteric site (not the active site). This causes the enzyme to change shape, altering the active site so the substrate can no longer fit.

What is a metabolic pathway vs. a multienzyme complex?

Metabolic Pathway: A chain of separate enzymes where the product of one becomes the substrate for the next. Multienzyme Complex: A group of separate enzymes physically attached to each other, passing the product directly along.

How does negative feedback regulate metabolic pathways?

The final product of the pathway acts as an allosteric inhibitor, binding to and turning off an enzyme early in the pathway to prevent overproduction.

What is the definition of cellular respiration?

A multistep metabolic pathway where organic molecules (like glucose) are broken down in a controlled manner by enzymes to release potential energy and synthesize ATP.

Are the processes of breaking down organic molecules in cellular respiration exergonic or endergonic?

Exergonic (energy-releasing). The energy released is then used to power the endergonic (energy-requiring) process of making ATP.

What is the difference between substrate-level phosphorylation and oxidative phosphorylation?

Substrate-level: Direct method of making ATP from the energy of a substrate. Oxidative: Indirect method where energy is first transferred to coenzymes (NAD⁺, FAD), which then deliver it to the electron transport system to make ATP.

What is the overall chemical equation for glucose oxidation?

C₆H₁₂O₆ + 6O₂ → 6CO₂ + 6H₂O

What are the four stages of cellular respiration and where does each occur?

1. Glycolysis: Cytosol (no oxygen required)

2. Intermediate Stage: Mitochondria (oxygen required)

3. Citric Acid Cycle: Mitochondria (oxygen required)

4. Electron Transport System: Mitochondria (oxygen required)

What is the initial substrate, final product, and net energy yield of glycolysis?

Initial Substrate: Glucose. Final Product: 2 Pyruvate molecules. Net Yield: 2 ATP and 2 NADH.

How is glycolysis regulated by negative feedback?

ATP acts as an allosteric inhibitor to turn off the enzyme phosphofructokinase (PFK) at step 3 when cellular energy levels are already high.

What is the structure of a mitochondrion?

A double-membrane organelle. The inner membrane has folds called cristae, the space between membranes is the outer compartment, and the innermost fluid is the matrix.

What happens during the Intermediate Stage of cellular respiration?

The multienzyme complex pyruvate dehydrogenase converts pyruvate and Coenzyme A into acetyl CoA, releasing CO₂ (decarboxylation) and forming 1 NADH per pyruvate (total of 2 NADH per glucose).

What is the net energy yield of one turn of the Citric Acid Cycle vs. one molecule of glucose?

One Turn (1 Acetyl CoA): 1 ATP, 3 NADH, 1 FADH₂. One Glucose (2 turns): 2 ATP, 6 NADH, 2 FADH₂.

Why is glucose completely disassembled by the end of the Citric Acid Cycle?

Because all 6 carbon atoms from the original glucose molecule have been fully broken down and released into the air as 6 CO₂ molecules.

What are the three main components embedded in the cristae of mitochondria for the ETS?

H⁺ (proton) pumps, electron carriers (ubiquinone/CoQ10 and cytochrome c), and ATP synthase.

What role does Oxygen (O₂) play in the electron transport system?

It acts as the final electron acceptor. It binds with electrons and hydrogen ions to produce water (H₂O).

How does ATP synthase actually manufacture ATP?

It harnesses the kinetic energy of hydrogen ions (H⁺) flowing down their concentration gradient from the outer compartment back into the matrix to bond Pᵢ to ADP.

How many ATP are generated by each NADH versus each FADH₂ in the electron transport chain?

1 NADH = 3 ATP (enters at the top pump). 1 FADH₂ = 2 ATP (enters at the second pump).

What is the theoretical vs. actual net yield of ATP from one glucose molecule?

Theoretical: 38 ATP. Actual Net Yield: 30 ATP (because energy is required to transport molecules from the cytosol into the mitochondria).

How does cyanide poisoning cause deadly "energy problems" in the body?

Cyanide binds to cytochrome c oxidase in the electron transport chain, completely blocking electrons from reaching oxygen and shutting down aerobic ATP production.

What happens to pyruvate if insufficient oxygen is available?

Lactate dehydrogenase converts pyruvate into lactate (lactic acid) in order to regenerate NAD⁺, allowing glycolysis to keep running to produce a small amount of ATP.

Why do low oxygen levels clinically correlate with low energy and lethargy?

Without oxygen, the cell cannot use its mitochondria and drops from making 30 net ATP per glucose down to only 2 net ATP via glycolysis (a 15-fold drop).

What is beta-oxidation?

The process where fatty acids are broken down 2 carbons at a time into acetyl CoA so they can enter the Citric Acid Cycle (this can only happen aerobically in the mitochondria).

Using ATP energy to contract a skeletal muscle is what type of energy conversion?

Chemical energy (stored in ATP bonds) to mechanical energy (muscle movement).

What type of reaction is an oxidation-reduction (redox) reaction?

An exchange reaction (because electrons are being swapped between molecules).

What is the general rule for how temperature affects enzyme activity?

Activity increases as temperature rises, but only up to a point (around 37°C to 40°C). If it gets too hot, the enzyme denatures (misshapes and breaks).

If ATP shuts down an enzyme by binding to a site other than the active site, it is acting as a what?

A noncompetitive (allosteric) inhibitor.

True or False: Enzymes are used up or destroyed after a single reaction.

False. Enzymes are reusable catalysts that remain unchanged after a reaction finishes.

What are the specific jobs of NAD⁺ and FAD?

They are coenzymes that act as cellular delivery trucks, picking up high-energy electrons and moving them to the electron transport system.

Which stage of cellular respiration works perfectly fine whether oxygen is high or low?

Glycolysis (it is completely anaerobic).

What does oxidative phosphorylation actually include?

1. Moving electrons down the transport chain to oxygen (O₂).

2. Coenzymes (NADH/FADH₂) dropping off electrons.

3. ATP synthase using an H⁺ gradient to build ATP.

Why does a damaged respiratory or cardiovascular system make you feel exhausted?

Less oxygen gets to your cells → cells can't run the mitochondria → ATP production drops from 30 net ATP down to just 2 net ATP per glucose.