Biochemistry Overview

ATP: The Cell's Energy Currency

• Role of ATP:

  • ATP (Adenosine Triphosphate) is utilized by cells for various forms of chemical work, including the synthesis of macromolecules.

  • It couples endergonic reactions (requiring energy input) with exergonic reactions (releasing energy) to provide the necessary energy.

• Mechanism of Energy Coupling:

  • ATP can integrate into a reaction as a reactant.

  • Alternatively, ATP can alter the shape of a reactant to facilitate the reaction.

  • A common method is phosphorylation, where a phosphate group is transferred from ATP to another molecule.

• ATP Structure and Energy Release:

  • ATP consists of adenosine bonded to three phosphate groups.

  • Each bond connecting these phosphate groups stores chemical energy.

  • When one phosphate bond is broken, energy is released, and ATP is hydrolyzed into ADP (Adenosine Diphosphate) and an inorganic phosphate group (Pi):
    ATP \rightarrow ADP + Pi + Energy

• Coupled Reaction Example:

  • For a reaction, such as a molecule 'C' reacting with 'D', to proceed, the energy released from ATP breaking down to ADP can be directly used:
    C + D + ATP \rightarrow Products + ADP + P_i

  • Without this coupled reaction, there would be no immediate source for the required energy.

Enzymes as Biological Catalysts

• Definition: Enzymes are typically proteins that function as catalysts, meaning they speed up chemical reactions within the cell.

• Function and Activation Energy:

  • Enzymes reduce the energy of activation required for a reaction to occur.

  • While enzymes significantly accelerate reactions, their presence alone does not guarantee a reaction will happen; it still depends on the overall free energy.

• Analogy: Catalysis is likened to lighting a match to wood; the act of applying the match (enzyme) lowers the energy needed to start the fire (reaction).

• Impact on Reaction: Enzymes do not alter the final products or the overall free energy change (\Delta G) of a reaction. They only make the reaction proceed faster.

• Graphical Representation:

  • A graph illustrating free energy (y-axis) versus reaction progress (x-axis) shows that a reaction without an enzyme requires a higher activation energy peak compared to the same reaction with an enzyme (lower peak).

• Enzyme Mechanism:

  • Enzymes act by binding to specific substrates at their active site to form an enzyme-substrate complex.

  • After the reaction, the enzyme releases the product(s).

  • Enzymes are not consumed or altered during the reaction process; they are released unchanged and are reusable, meaning they can catalyze multiple reactions.

• Specificity and Naming:

  • Enzymes are highly specific to their substrates.

  • They are often named by adding the suffix "-ase" to the name of their substrate (e.g., an enzyme acting on lipids is called a lipase). This specificity is due to the unique shape of their active site.

Factors Affecting Enzyme Activity

• Enzyme Presence: The primary factor, as enzymes significantly lower the activation energy, making reactions much faster.

• Substrate Concentration:

  • A higher concentration of substrate molecules increases the likelihood of them binding to enzyme active sites, leading to a faster reaction rate until the enzymes become saturated.

• Temperature:

  • Reaction rates generally increase with temperature due to increased molecular collision frequency, similar to diffusion.

  • However, beyond an optimal temperature, enzymes (being proteins) will begin to denature (lose their specific three-dimensional structure and thus their function).

  • Each enzyme has a specific optimal temperature. For instance, enzymes in thermophilic organisms (like certain bacteria and archaea) function optimally at much higher temperatures than human enzymes, enabling them to thrive in extreme environments.

• pH:

  • Each enzyme has an optimal pH range where its activity is maximal.

  • Deviations from this optimal pH can alter the enzyme's structure, leading to denaturation and reduced activity.

  • Example: Pepsin, an enzyme found in the human stomach, is active in a highly acidic environment, with an optimal pH ranging between roughly 0 and 4.

• Enzyme Activation/Inhibition:

  • Inhibition: Certain molecules can reduce or block enzyme activity.

    • Example: Penicillin is an antibiotic that works by blocking a specific enzyme in bacteria, which disrupts their cellular processes.

  • Feedback Inhibition: A mechanism where the product of a metabolic pathway inhibits an enzyme early in the pathway, regulating its own production.

• Enzyme Cofactors:

  • These are non-protein helper ions or molecules that assist enzymes in their catalytic activity.

Oxidation-Reduction (Redox) Reactions

• Fundamentals: Redox reactions are coupled chemical reactions involving the transfer of electrons between reactants.

• Definitions:

  • Oxidation: The loss of electrons by a substance (often remembered by LEO: Lose Electrons, Oxidized).

  • Reduction: The gain of electrons by a substance (often remembered by GER: Gain Electrons, Reduced).

  • These always occur together; if one substance loses electrons (oxidized), another must gain them (reduced).

• Example 1: Oxygen and Magnesium:

  • When oxygen combines with magnesium:

    • Oxygen gains electrons and becomes reduced.

    • Magnesium loses electrons and becomes oxidized.

  • This electron exchange forms the chemical bond.

• Example 2: Sodium Chloride (NaCl) Formation:

  • Sodium (Na) and Chlorine (Cl) form table salt (NaCl). In the formation of NaCl:

    • Sodium (Na) loses an electron to become a positive ion (Na^+), thus it is oxidized.

    • Chlorine (Cl) gains an electron to become a negative ion (Cl^-), thus it is reduced.

Cellular Respiration: Producing ATP

• Purpose: Cellular respiration is a metabolic pathway that uses carbohydrates (e.g., glucose) to generate ATP, the cell's energy currency.

• Relationship to Photosynthesis: It is essentially the opposite process of photosynthesis.

• Overall Reaction:

  • It consumes glucose and oxygen to produce carbon dioxide, water, and a significant amount of energy in the form of ATP:
    C6H{12}O6 (Glucose) + 6O2 (Oxygen) \rightarrow 6CO2 (Carbon Dioxide) + 6H2O (Water) + Energy (ATP)

• Interdependence with Photosynthesis:

  • The products of photosynthesis (glucose and oxygen), created in chloroplasts, become the reactants for cellular respiration in the mitochondria.

  • Conversely, the carbon dioxide released by mitochondria during cellular respiration is a reactant for photosynthesis in plants.

• Food and Energy Flow: Our food, derived from plants or animals that consume plants, provides the necessary nutrients (like glucose) and oxygen that are delivered to our mitochondria to produce ATP.