Energy, Chemical Reactions, Enzymes, Metabolism, and Protein Synthesis in Biological Systems

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4.1 Energy in Biological Systems

Properties of Living Organisms

Living organisms exhibit several defining properties that distinguish them from non-living matter. These properties are essential for the maintenance of life and include:

Organization: Living things are highly organized, from the molecular to the organismal level.
Metabolism: The sum of all chemical reactions that occur within an organism.
Homeostasis: The ability to maintain a stable internal environment.
Growth and Development: Organisms grow and develop according to specific instructions coded in their DNA.
Reproduction: The ability to produce new individuals.
Response to Stimuli: The ability to respond to environmental changes.
Adaptation through Evolution: Populations evolve over generations.

Energy Capture and Storage in Plants and Animals

Plants and animals differ in how they capture and store energy:

Plants capture energy from sunlight through photosynthesis, converting light energy into chemical energy stored in glucose.
Animals obtain energy by consuming organic molecules and storing energy in the form of glycogen and fat.

Energy Is Used to Perform Work

Energy is required for all biological work, which can be classified as:

Chemical work: Synthesis of complex molecules.
Transport work: Movement of substances across cell membranes.
Mechanical work: Movement of muscles or cellular structures.

Forms of Energy: Kinetic and Potential

Energy exists in two main forms:

Kinetic energy: The energy of motion (e.g., movement of molecules).
Potential energy: Stored energy due to position or structure (e.g., chemical bonds).

Example: A ball at the top of a hill has potential energy; as it rolls down, this is converted to kinetic energy.

Energy Conversion and Loss

Energy can be converted from one form to another, but some energy is always lost as heat during these conversions, as described by the laws of thermodynamics.

First Law of Thermodynamics: Energy cannot be created or destroyed, only transformed.
Second Law of Thermodynamics: Every energy transfer increases the entropy (disorder) of the universe.

Entropy is a measure of disorder or randomness in a system.

Potential Energy Storage in Biological Systems

Potential energy is stored in the chemical bonds of molecules such as ATP, glucose, and lipids.

4.2 Chemical Reactions

Energy Transfer between Molecules

Chemical reactions involve the transformation of reactants into products, often with the transfer of energy. Key terms:

Reactant: A starting substance in a chemical reaction.
Product: The substance(s) formed by the reaction.
Substrate: The specific reactant acted upon by an enzyme.

Measuring Reaction Rates

The rate of a chemical reaction is measured by the change in concentration of reactants or products per unit time.

Free Energy and Chemical Bonds

Free energy is the energy available to do work. The formation or breaking of chemical bonds involves changes in free energy.

Activation Energy

Activation energy is the minimum energy required to initiate a chemical reaction.

Endergonic vs. Exergonic Reactions

Type	Energy Change	Example
Endergonic	Absorbs energy (ΔG > 0)	Synthesis of glucose
Exergonic	Releases energy (ΔG < 0)	Hydrolysis of ATP

In exergonic reactions, products have less free energy than reactants; in endergonic reactions, products have more free energy.

Reversible and Irreversible Reactions

Reversible reactions can proceed in both directions, while irreversible reactions proceed in one direction only. The net free energy change (ΔG) determines reversibility.

4.3 Enzymes

Definition and Function

Enzymes are biological catalysts, usually proteins, that speed up chemical reactions without being consumed. Substrates are the molecules upon which enzymes act.

Isozymes

Isozymes are different forms of an enzyme that catalyze the same reaction but may differ in structure or regulatory properties. They are useful in medical diagnoses as biomarkers for tissue damage.

Factors Affecting Enzyme Activity

Temperature and pH can alter enzyme activity.
Substrate concentration and enzyme concentration also affect reaction rates.
Enzymes can be activated, inactivated, or modulated by cofactors, coenzymes, or inhibitors.

Coenzymes and Vitamins

Coenzymes are organic molecules that assist enzymes, often derived from vitamins.

Enzyme Inactivation

Enzymes can be inactivated by denaturation (loss of structure) or by inhibitors.

Enzymatic Reaction Categories

Category	Description	Example
Oxidation-Reduction	Transfer of electrons	Cellular respiration
Hydrolysis-Dehydration	Adding/removing water	Digestion of proteins
Addition-Subtraction-Exchange	Transfer of functional groups	Phosphorylation
Ligation	Joining two molecules	DNA synthesis

4.4 Metabolism

Definition and Types

Metabolism is the sum of all chemical reactions in the body. It includes:

Anabolic reactions: Build complex molecules from simpler ones (require energy).
Catabolic reactions: Break down complex molecules into simpler ones (release energy).

Calorie (kcal) is a unit of energy; 1 kcal is the amount of energy needed to raise 1 kg of water by 1°C.

Metabolic Pathways

A metabolic pathway is a series of enzyme-catalyzed reactions. Intermediates are molecules formed between the start and end of a pathway.

Regulation of Metabolism

Cells regulate metabolism by:

Controlling enzyme concentrations
Producing modulators
Using different enzymes for reversible reactions
Compartmentalizing enzymes
Maintaining ATP/ADP ratios

ATP: Structure and Function

ATP (adenosine triphosphate) is the primary energy carrier in cells. It consists of adenine, ribose, and three phosphate groups. Hydrolysis of ATP releases energy:

Aerobic vs. Anaerobic Pathways

Pathway	Oxygen Required?	ATP Yield
Aerobic	Yes	30-32 ATP/glucose
Anaerobic	No	2 ATP/glucose

Key Metabolic Pathways

Glycolysis: Converts glucose to pyruvate, produces ATP and NADH.
Krebs Cycle: Processes acetyl-CoA, produces NADH, FADH2, and ATP.
Electron Transport System (ETS): Uses NADH and FADH2 to produce ATP via oxidative phosphorylation.

Branch Points and Net Yields

Pyruvate is a branch point: it can enter aerobic pathways (Krebs cycle) or anaerobic pathways (lactate fermentation). Net ATP yield varies depending on the pathway.

Proteins and Genetic Information

Protein Structure and Function

Proteins are highly variable and specific due to the sequence of amino acids, which determines their three-dimensional structure and function.

Genetic Code and Protein Synthesis

Gene: A segment of DNA that codes for a protein.
Codon: A sequence of three nucleotides in mRNA that specifies an amino acid.
Constitutive genes: Always expressed.
Regulated genes: Expressed as needed.

Protein Synthesis Process

Transcription: DNA is transcribed to mRNA by RNA polymerase.
RNA Processing: Introns are removed, exons are spliced together, and a 5' cap and poly-A tail are added.
Translation: mRNA is translated into protein at the ribosome, with tRNA bringing amino acids to the growing chain.

Alternative Splicing

Alternative splicing allows a single gene to code for multiple proteins by rearranging exons during mRNA processing.

Protein Sorting and Targeting

Proteins with a signal sequence are directed to specific cellular locations. Proteins lacking a targeting sequence remain in the cytosol.

Posttranslational Modifications

Modification	Description	Example
Cleavage	Cutting of peptide bonds	Activation of insulin
Glycosylation	Addition of carbohydrate groups	Glycoproteins
Phosphorylation	Addition of phosphate groups	Enzyme regulation
Assembly	Formation of polymeric proteins	Collagen fibers