The Use of Energy by Cells Practice Flashcards

Metabolism and the Principles of Biological Energy

Composition of Cellular Metabolism: Catabolic and anabolic pathways together constitute the cell’s metabolism.
Energy Transfer in Cells: A major portion of the energy stored in the chemical bonds of food molecules is dissipated as heat. However, some of this energy is successfully converted into useful forms needed to drive the synthesis of new molecules.
Forms of Energy Conversion: Cells convert energy from one form to another. Specifically, photosynthetic organisms use sunlight to synthesize organic molecules. These molecules pass to animals and microorganisms, as well as into organic material in soil and oceans. Carbon atoms cycle continuously through the biosphere.
Restoration of Carbon: Carbon is ultimately restored to the atmosphere in the form of $CO_2$ when organic molecules are oxidized by cells or by the burning of fossil fuels.
Biological Order: Biological structures are highly ordered. Biological order is made possible by the release of heat energy from cells. Cells take in energy from their environment and use it to generate order within themselves.

Oxidation and Reduction (Redox Reactions)

Definitions:
- Oxidation: Defined as the removal of electrons. When an atom ends up with a lesser share of electrons, it is said to be oxidized.
- Reduction: Represents a gain of electrons. When an atom ends up with a greater share of electrons (represented visually by blue clouds in polar covalent bonds), it is said to be reduced.
Carbon Compound Oxidation: A simple reduced carbon compound, such as methane ( $CH_4$ ), can be oxidized in a stepwise fashion through the successive replacement of its covalently bonded hydrogen atoms with oxygen atoms.

Free Energy and Catalysis

Free Energy ( $G$ ): Measures the energy of a molecule that could in principle be used to do useful work at a constant temperature ( $kJ/mol$ ). Energy can also be expressed in calories ( $1 \text{ joule} = 0.24 \text{ calories}$ ).
The Second Law of Thermodynamics: The disorder of the universe can only increase. A chemical reaction occurs spontaneously only if the change in free energy, $\Delta G$ , is negative (\Delta G < 0).
Reaction Predictors: To predict the outcome of a reaction, the standard free-energy change ( $\Delta G^\circ$ ) must be determined. This represents the gain or loss of free energy as one mole of reactant is converted to one mole of product under standard conditions:
- Aqueous solution concentration: $1 \text{ M}$
- $pH$ : $7.0$
Equilibrium Constant ( $K$ ): A fixed relationship exists between $\Delta G^\circ$ and $K$ . For a reversible reaction $Y \rightleftharpoons X$ , the reaction proceeds until the ratio of concentrations $[X]/[Y]$ is equal to $K$ .
- Formula at $37 \text{ °C}$ : $\Delta G^\circ = -5.94 \log_{10} K$
- Formula for $K$ : $K = 10^{-\Delta G^\circ / 5.94}$
Enzyme Function: Enzymes act as catalysts to reduce the activation energy required to initiate spontaneous reactions. They convert substrates to products while remaining unchanged themselves. They speed up the rate but do not change the $\Delta G$ of the reaction.
Activation Energy: Even energetically favorable reactions require activation energy to start.
- Reaction $Y \rightarrow X$ (favorable): Requires activation energy (energy $a$ minus energy $b$ ).
- Reverse reaction $X \rightarrow Y$ (unfavorable): Requires a much larger activation energy (energy $a$ minus energy $c$ ).
Reaction Coupling: An energetically unfavorable reaction (\Delta G > 0) such as $X \rightarrow Y$ cannot occur unless it is coupled to an energetically favorable reaction (\Delta G < 0) such as $C \rightarrow D$ , provided the net free-energy change for the pair is negative (less than $0$ ).

Activated Carriers and Biosynthesis

Mechanism of Activated Carriers: The formation of an activated carrier is coupled to an energetically favorable reaction. These carriers store and transfer energy in a form cells can use.
ATP (Adenosine 5'-triphosphate):
- The most widely used activated carrier.
- Energy is stored in "high-energy" phosphoanhydride bonds between the two outermost phosphate groups.
- Hydrolysis Reaction: $ATP + H_2O \rightarrow ADP + P_i + \text{free energy}$
- Standard $\Delta G^∘$ for ATP hydrolysis: $-30.5 \text{ kJ/mol}$ .
NADH and NADPH: Both are activated carriers of electrons.
- NADPH: Primarily used in biosynthetic (anabolic) reactions.
- NADH: Often involved in catabolic reactions leading to the production of ATP.
- Mechanics: $NADP^+$ receives two electrons as one hydrogen atom plus an electron (a hydride ion, $H^-$ ) to become $NADPH$ .
Acetyl Coenzyme A (CoA):
- The sulfur atom forms a high-energy thioester bond to acetate.
- Hydrolysis of this bond releases a large amount of free energy, allowing the acetyl group to be transferred easily to other molecules.
Overview of Activated Carriers:
- ATP: Carries phosphate in high-energy linkage.
- NADH, NADPH, FADH2: Carry electrons and hydrogen.
- Acetyl CoA: Carries an acetyl group.
- Carboxylated biotin: Carries a carboxyl group.
- S-adenosylmethionine: Carries a methyl group.
- Uridine diphosphate glucose: Carries glucose.

The Glycolytic Pathway

Location: Occurs in the cytoplasm.
ATP Usage and Generation:
- Two reactions consume ATP (producing ADP and phosphorylated sugars).
- Two reactions generate ATP via substrate-level phosphorylation.
Yield: One reaction yields $NADH$ by reduction of $NAD^+$ .
Irreversibility: Steps 1, 3, and 10 are essentially irreversible under ordinary cell conditions due to large negative $\Delta G$ values.
Fate of Pyruvate:
- Anaerobic Metabolism (Fermentation): Purpose is to regenerate $NAD^+$ so glycolysis can continue. In muscle cells, pyruvate becomes lactic acid. In yeast, it becomes ethanol and $CO_2$ .
- Aerobic Metabolism: Pyruvate is transported into the mitochondria and linked to coenzyme A to form Acetyl CoA.
Warburg Effect (1924): Otto Warburg observed a shift from oxidative phosphorylation to aerobic glycolysis (fermentation) in animal tumors, even in the presence of oxygen.

Mitochondrial Structure and compartments

Four Compartments:
1. Outer Membrane: Contains pores (porins) allowing passive diffusion of molecules up to $500 \text{ kDa}$ .
2. Inner Membrane: Composed of three distinct domains:
  - Boundary membrane: Flat area below the outer membrane.
  - Cristae: Sheetlike/tubelike invaginations.
  - Crista junctions: Sharp bends connecting the boundary membrane to cristae.
3. Intermembrane Space: Continuous with the lumen of the cristae.
4. Matrix: Contains the Citric Acid Cycle, mitochondrial DNA, ribosomes, and granules.

The Citric Acid Cycle and Fatty Acid Oxidation

Pyruvate Transport: The Mitochondrial Pyruvate Carrier (MPC) is a hetero-dimer ( $MPC1/MPC2$ ). Pyruvate is co-transported with a proton.
TCA Cycle Overview: The acetyl group in Acetyl CoA is oxidized to $CO_2$ . Energy is temporarily stored in reduced $NADH$ and $FADH_2$ .
Fatty Acid Oxidation:
- Short- to long-chain fatty acids are oxidized in mitochondria to produce ATP.
- Very long-chain fatty acids are oxidized in peroxisomes, producing heat rather than ATP.
Malate-Aspartate Shuttle: Helps maintain correct cytosolic and matrix concentrations of $NAD^+$ and $NADH$ by transferring electrons across the inner membrane.

The Mitochondrial Electron-Transport Chain (ETC)

Electron Flow: Path follows: Complex I → Coenzyme Q → Complex III → Cytochrome c → Complex IV → $O_2$ (→ $H_2O$ ).
Complexes:
- Complex I: NADH donates two electrons via FMN and iron-sulfur clusters to CoQ. The movement of electrons causes a piston-like horizontal movement of the $t$ -helix, pumping four protons across the membrane.
- Coenzyme Q (CoQ): Lipid-soluble carrier. Oxidized form is CoQ; reduced form is $CoQH_2$ .
- Cytochrome c (cyt c): Water-soluble carrier.
Reduction Potentials ( $E^{\circ \prime}$ ): Increase from $NADH$ ( $-320 \text{ mV}$ ) to $O_2$ ( $+860 \text{ mV}$ ). This favors spontaneous electron flow.
Q Cycle: An evolutionarily conserved mechanism in Complex III that optimizes proton pumping per pair of electrons. Oxidation of one $CoQH_2$ transfers four protons to the intermembrane space and two electrons to two cytochrome c molecules.

ATP Synthase and Chemiosmosis

Chemiosmosis: The proton-motive force (PMF) generated by pumping protons across a membrane powers ATP synthesis. Protons flow down their electrochemical gradient through the ATP synthase ( $F_0 F_1$ complex).
Structure of ATP Synthase:
- F0: The rotating portion embedded in the membrane; contains the $c$ ring.
- F1: The stationary ATPase head. Contains the $\gamma$ subunit (rotates) and $\beta$ subunits (site of synthesis).
Binding-Change Mechanism:
- O (Open) state: Binds ATP poorly, binds ADP and $P_i$ weakly.
- L (Loose) state: Binds ADP and $P_i$ more strongly; cannot bind ATP.
- T (Tight) state: Binds ADP and $P_i$ tightly enough to spontaneously form ATP.
Reversibility: ATP synthase is a reversible coupling device. If the proton gradient falls too low, it will hydrolyze ATP to pump protons and rebuild the gradient.

Energy Yield Summary and Regulation

Product Yields from One Glucose Molecule:
- Glycolysis: $2 \text{ NADH (cytosolic)}$ , $2 \text{ ATP}$ .
- Pyruvate Oxidation: $2 \text{ NADH (matrix)}$ .
- Citric Acid Cycle: $6 \text{ NADH (matrix)}$ , $2 \text{ FADH}_2$ , $2 \text{ GTP (ATP equivalence)}$ .
- Total ATP Yield: Approximately $30 \text{ ATP}$ .
- Note: Cytosolic $NADH$ yields fewer ATP than matrix $NADH$ because energy is required to transport electrons into the matrix across the impermeable membrane.
Uncoupling Proteins (UCPs): These proteins allow protons to flow back across the inner membrane without passing through ATP synthase, dissipating energy as heat.
DNP (2,4-dinitrophenol): A deadly chemical uncoupling agent used illegally for weight loss ("the dangerous diet pill"). It disrupts the proton-motive force, preventing ATP synthesis and causing fatal hyperthermia.

Questions & Discussion

Q: In which of the following reactions does the red atom undergo an oxidation?

$Na \rightarrow Na^+$ (Na atom to Na+ ion)
$Cl \rightarrow Cl^-$ (Cl atom to Cl- ion)
$CH_3CH_2OH \rightarrow CH_3CHO$ (ethanol to acetaldehyde)
$CH_3CHO \rightarrow CH_3COO^-$ (acetaldehyde to acetic acid)
$CH_2=CH_2 \rightarrow CH_3CH_3$ (ethene to ethane) A: Oxidation is the removal of electrons.

$Na \rightarrow Na^+$ is oxidation (loss of an electron).
ethanol → acetaldehyde is oxidation (loss of hydrogens/electrons).
acetaldehyde → acetic acid is oxidation (gain of oxygen/loss of electrons).

Q: What features are shared by photosynthesis and respiration?

Production of NADH
Production of ATP
Production of sugar
Production of oxygen A: Both processes generate ATP.

Q: What is the main purpose of the Malate-Aspartate shuttle to cells?A: The transfer of electrons from cytosolic NADH across the inner mitochondrial membrane.

Q: Which of the following is NOT true of chemiosmosis?

ATP synthase generates ATP from ADP and $P_i$
It produces the majority of ATP in a cell
The proton-motive force is used to synthesize ATP
It requires oxygen A: It requires oxygen is not strictly true of chemiosmosis itself (though it is required for aerobic respiration), as chemiosmosis can occur in anaerobic environments or via photosynthesis.

Exam 1 Study Objectives

Compare oxidative phosphorylation location: Eukaryotic cells (mitochondria) vs. Bacteria (plasma membrane).
Describe the structure and compartment functions of the mitochondrion.
Explain how pyruvate and fatty acids move into the matrix (MPC and transporters).
Understand why $NADH$ does not donate electrons directly to molecular oxygen in living systems (requires the ETC for controlled energy release).
List ETC components in order and describe their electron affinities (affinity increases along the chain).
Distinguish between substrate-level phosphorylation and oxidative phosphorylation.
Learn how fermentation (anaerobic) contrasts with respiration (aerobic).
Understand how chemiosmosis works in mitochondria, chloroplasts, and bacteria.

Stage I – Cytosol:
- Glucose is converted to pyruvate through glycolysis.
- Fatty acids are converted to fatty acyl CoA.
- Pyruvate and fatty acyl CoA diffuse through porins into the mitochondrion.
- Inner membrane transport proteins facilitate the transport of pyruvate and fatty acids into the matrix.
- Cytosolic NADH electrons are shuttled to NAD+ in the matrix.
Stage II – Mitochondrial Matrix:
- Pyruvate is converted to acetyl CoA with the formation of NADH and CO2 (which diffuses out of mitochondrion and cell).
- Fatty acyl CoA undergoes conversion of two carbons to acetyl CoA, generating FADH2 and NADH.
- Acetyl CoA oxidation in the citric acid cycle produces NADH, FADH2, GTP, and CO2.
Stage III – Inner Membrane:
- NADH and FADH2 transfer energetic electrons to the electron transport chain (ETC).
- Electrons are transferred through electron-transport complexes to O2 (which diffuses into the cell and mitochondrion matrix).
- Electrons from NADH flow directly from complex I to complex III, bypassing complex II. Electrons from FADH2 flow from complex II to complex III, bypassing complex I.
- Energy released during electron movement through complexes drives protons (H+) transport from the matrix to the intermembrane space, generating electrical and concentration gradients that constitute the proton-motive force.
Stage IV – Inner Membrane and Matrix:
- The F0F1 ATP synthase harnesses the proton-motive force energy to regenerate ATP in the matrix.
- Antiporter proteins import ADP and Pi into the matrix, coupled to the export of hydroxyl groups and ATP.