Energy, Chemical Reactions, and Cellular Respiration

3.1a Classes of Energy

Energy: the capacity to do work.
- Potential energy: stored energy (energy of position).
  - Chemical bonds store energy.
  - Concentration gradient of plasma membrane.
- Kinetic energy: energy of motion.
Potential energy and the plasma membrane
- Concentration gradient exists across the plasma membrane.
- Boundary between the inside and outside of the cell.
Potential energy and electron shells
- Electrons move from a higher- to lower-energy shell.
- Kinetic energy can be harnessed to do work.
- This occurs in the Electron Transport Chain of cellular respiration.
Potential energy must be converted to kinetic energy before it can do work.

3.1b Forms of Energy

Chemical energy: a form of potential energy found in the chemical bonds of a substance.
Types of kinetic energy:
- Electrical energy: a form of kinetic energy due to the movement of charged particles.
  - E.g., electricity or the movement of ions across the plasma membrane of a neuron.
- Mechanical energy: exhibited by objects in motion due to an applied force.
  - E.g., muscle contraction for walking.

3.2a Chemical Equations

Metabolism: the sum of all biochemical reactions in living organisms.
Chemical reactions: chemical bonds are broken or formed.
- Reactants: substances present at the start of a chemical reaction.
- Products: substances formed by the reaction.
- $A + B \rightarrow C$
Three ways to classify chemical reactions:
1. Change in chemical structure.
2. Change in chemical energy.
3. Is the reaction reversible or irreversible?

3.2b Classification of Chemical Reactions: Change in Chemical Structure

Decomposition reaction (catabolism/catabolic reactions)
- An initial large molecule is broken down into smaller structures.
- $AB \rightarrow A + B$
- Includes hydrolysis.
Synthesis reaction (anabolism/anabolic reactions)
- Two or more structures are combined to form a larger structure.
- $A + B \rightarrow AB$
- Includes dehydration synthesis.
Exchange reaction
- Groups are exchanged between two chemical structures.
- $AB + C \rightarrow A + BC$

3.2b Classification of Chemical Reactions: Oxidation-Reduction Reaction (Redox Reaction)

Electrons are moved from one chemical structure to another.
- The electron is "ENERGY"!!
Structure that loses an electron is oxidized during oxidation.
Structure that gains an electron is reduced during reduction.
Reactions always occur together.
Electrons may be moved alone or with a hydrogen ion.
- LEO: Loses Electron Oxidizing
- GER: Gains Electron Reducing
- OIL: Oxidation Is Losing
- RIG: Reduction Is Gaining
Nicotinamide adenine dinucleotide (NAD)
- $NAD+$ is the oxidized form, NADH is the reduced form.
- Which version of this molecule is energy-rich?
- And ready to give up its energy?
- This molecule is an important energy-releasing molecule in cellular respiration.

3.2b Classification of Chemical Reactions: Change in Chemical Energy

Exergonic reactions
- Energy is released with a net decrease in potential energy.
- E.g., decomposition reactions.
Endergonic reactions
- Energy is supplied with a net increase in potential energy.
- E.g., synthesis reactions.
ATP cycling
- ATP is formed by a dehydration reaction (endergonic) between ADP and Pi, and energy is supplied by the oxidation of fuel molecules.
- ATP is oxidized and split by hydrolysis (exergonic) to form ADP and Pi.

3.2b Classification of Chemical Reactions: Net Direction of Reaction - Reversible or Irreversible

Irreversible reaction
- Net loss of reactants and a net gain in products.
- $A + B \rightarrow AB$ or $AB \rightarrow A + B$
Reversible reaction
- No net gain or loss of either reactants or products; equal.
- Remains in equilibrium $A + B \leftrightarrow AB$
- $CO2 + H2O \leftrightarrow H2CO3 \leftrightarrow H^+ + HCO_3^-$
 - Carbon dioxide, water, carbonic acid, bicarbonate ion, $H^+$ ion.
 - Blood transport of $CO_2$ and acid-base balance.

3.2c Reaction Rates and Activation Energy

Reaction rate: measure of how quickly a chemical reaction takes place.
Activation energy ( $E_a$ )
- Minimum energy required to break existing chemical bonds.
Increasing temperature in the lab can overcome activation energy; however…
- A significant temperature increase in a cell would denature proteins.
- Therefore, protein catalysts called enzymes are used instead.

3.3a Function of Enzymes

Enzymes
- Catalysts that accelerate normal physiologic activities.
- Decrease the activation energy of cellular reactions.
- Only facilitate reactions that would already occur.

3.3b Enzymes Structure and Location

Most enzymes are globular proteins.
- Three-dimensional shape with active site specificity where reactants attach.
- Forms enzyme-substrate complex.
Enzymes can be:
- Within the cell
- In the plasma membrane
- Secreted from the cell

3.3c Mechanism of Enzyme Action

Enzyme catalysis
1. Substrate enters active site, forming enzyme-substrate complex.
2. Enzyme changes shape slightly, resulting in an even closer fit (induced fit model).
3. Change in enzyme shape stresses chemical bonds, permitting new bonds to be formed.
4. Products are released; the enzyme likely repeats the process.

3.3c Mechanism of Enzyme Action and 3.3d Classification and Naming of Enzymes

Cofactors: non-protein organic or inorganic structure.
- Molecules or “helper” ions are often required for the reaction.
- Organic cofactors are coenzymes.
Naming: usually ends in –ase
- May tell you what it does or what it’s doing.
- Oxidoreductase
- Transferase
- Hydrolase: protease or lipase
- Ligase

3.3e Enzymes and Reaction Rates Factors that Influence Reaction Rates

Substrate concentration
- Enzyme saturation
Temperature
pH
Activation energy

3.3f Controlling Enzymes

Inhibitors:
- Competitive
- Noncompetitive

3.3g Metabolic Pathways and Multienzyme Complexes

Metabolic pathway: Multiple enzymes are usually required to convert the initial substrate to the final product.
- E.g., chemical breakdown of glucose.
Regulation of enzymes
- Phosphorylation: addition of phosphate group.
  - Important in cellular respiration/glucose oxidation
- Dephosphorylation: removal of phosphate group.

3.4 Cellular Respiration & 3.4a Glucose Oxidation

Exergonic metabolic pathway that releases electrons (oxidation) and energy used to synthesize ATP (endergonic).
Oxygen is required for maximum ATP.
- Oxygen is the final electron ACCEPTOR in cellular respiration!
- Without an “acceptor” to remove the electrons, the electron transport chain STOPS, and no energy is produced.
- Very little ATP is produced without oxygen, and one will die in minutes without oxygen!!
Can use a variety of molecules to form ATP, but the best is…
Glucose oxidation: $C6H{12}O6 + 6 O2 \rightarrow 6 CO2 + 6 H2O$

3.4a Overview of Glucose Oxidation

Two pathways for ATP production
- Energy to attach phosphate group to ADP
  1. Substrate-level phosphorylation: Energy can be used directly.
    - Least common
  2. Oxidative phosphorylation: Energy is used indirectly.
    - Most common
    - Energy is first released to coenzymes ( $NAD^+$ & FAD) and then transferred to form ATP.
Requires 20 different enzymes, working in either the cytosol or mitochondria.

3.4a Overview of Glucose Oxidation

Four stages of glucose oxidation:
1. Glycolysis
  - In the cytosol
  - Does not require $O_2$
2. Intermediate stage
  - In the mitochondria matrix
  - Requires $O_2$
3. Citric acid cycle
  - In the mitochondria matrix
  - Requires $O_2$
4. Electron transport system
  - In the mitochondria cristae
  - Requires $O_2$
- Cytoplasm = cytosol + organelles

3.4b Glycolysis

Steps 1–5
- Glucose is split into two molecules of glyceraldehyde 3-phosphate (G3P).
- ATP is “invested” at steps 1 and 3
  - Phosphate groups are transferred to break down products of glucose.
Steps 6–7
- Occur twice in glucose oxidation
- Step 6: unattached Pi is added to the substrate; two hydrogen atoms are released to $NAD^+$
- Step 7: Pi is transferred to ADP to form ATP
Steps 8–10
- Occur twice in glucose oxidation
- Step 8: molecule from step 7 is converted to an isomer
- Step 9: loss of water molecule
- Step 10: Pi is transferred to form ATP
Summary of Glycolysis
- Metabolic process, occurs in the cytosol, does not require oxygen
- Glucose is the initial substrate (6 carbons).
- Pyruvate is the final product (2 pyruvate molecules; 3 carbons each).
  - If $O_2$ is available, pyruvate enters the mitochondria and continues to the intermediate stage.
  - If $O_2$ is not available, pyruvate is converted to lactate.
    - Anaerobic
    - Only TWO net ATP are formed in glucose oxidation if oxygen is not available.
- Net 2 ATP formed (2 invested, 4 formed)
- 2 NADH formed

3.4c Intermediate Stage

Occurs in the matrix of the mitochondria
Pyruvate (2 were formed) and coenzyme A (CoA; already in the matrix) combine to form acetyl CoA.
- Acetyl CoA (product) enters the citric acid cycle.
Products generated:
- 2 acetyl CoA
- 2 $CO_2$
- 2 NADH
- NO ATP GENERATED

3.4d Citric Acid Cycle (Krebs Cycle)

Cyclic metabolic pathway
- Occurs in the mitochondria matrix; requires $O_2$
Acetyl CoA combines with oxaloacetate (OAA) to form citrate.
- OAA is regenerated
1 ATP, 3 NADH, and 1 $FADH2$ are formed, and 2 $CO2$ are released during each cycle.
- Two turns of the cycle must occur since 2 pyruvate molecules were produced in glycolysis.
Products generated
- Citrate (citrate + $H^+$ → citric acid)
- 4 $CO_2$ (2 per cycle)
- 6 NADH (3 per cycle)
- 2 $FADH_2$ (1 per cycle)
- 2 ATP (1 per cycle)
Glucose is now fully digested
- 6 carbons of glucose are released as 6 $CO_2$ molecules
  - (2: intermediate stage; 4: citric acid cycle)

3.4d Summary of Glycolysis, Intermediate Stage, and Citric Acid Cycle

From each glucose molecule using substrate-level phosphorylation:
- 4 ATP are made
- 10 NADH and 2 $FADH_2$ are made
- 6 $CO_2$ molecules are made
To consider… why are NADH and $FADH_2$ produced instead of $NAD^+$ and FAD??
- Which pair of molecules are “reduced” and have electrons that can be used as energy later?

3.4e The Electron Transport System

GOAL: transfer of electrons (energy) from coenzymes NADH and $FADH_2$ to make ATP
Electron transport chain: series of $H^+$ (proton) pumps and electron carriers found within the mitochondria cristae
1. Electrons are transferred from NADH and $FADH_2$ to electron carriers in the cristae
2. Oxygen “accepts” these electrons after they’ve moved through the chain, producing water
  - Without $O_2$ to “accept” the electrons, the electron movement through the chain stops; no kinetic energy is produced in the next step; end of the process
3. The kinetic energy of electrons moving or “falling” through the chain is harnessed by $H^+$ (proton) pumps that produce a proton gradient across the mitochondrial cristae.
  - Active transport of $H^+$ up the gradient
4. The $H^+$ concentration gradient established across the mitochondrial matrix is potential energy
5. This potential energy is harnessed or used by ATP synthase (enzyme) to add P to ADP to produce ATP

3.4e The Electron Transport System & 3.4f ATP production

Oxidative phosphorylation
- Oxygen is the final electron acceptor
- ATP is formed from phosphorylation of ADP using energy from electrons
ATP produced:
- Electrons from NADH enter at the top
  - Passed through 3 $H^+$ pumps
  - Generates 3 ATP molecules
- Electrons from $FADH_2$ enter at the second pump
  - Generates 2 ATP molecules
- # of pumps passed thru = # ATP produced

3.4f ATP Production

ATP in glucose breakdown

Stage/Total	Substrate-level phosphorylation	Oxidative phosphorylation	Total
Glycolysis	2 ATP	2 NADH → 6 ATP
Intermediate Stage	––	2 NADH → 6 ATP
Citric Acid Cycle	2 ATP	6 NADH → 18 ATP
		2 $FADH_2$ → 4 ATP
Stage Total	4 ATP	34 ATP
OVERALL TOTAL ATP			38

Several ATP are used to move molecules around the cell (e.g., from cytosol to mitochondria) during the process…

NET ATP = 30