Proteins, Energy, and Enzymes: Structure, Function, and Biological Roles

Proteins, Energy, and Enzymes

Introduction

This study guide covers the structure and function of proteins, the principles of energy in biological systems, and the role of enzymes in catalyzing biochemical reactions. These topics are fundamental to understanding cellular processes in General Biology.

Macromolecules and Polymers

Dehydration and Hydrolysis Reactions

Macromolecules such as proteins, carbohydrates, and nucleic acids are formed by linking smaller units (monomers) into larger chains (polymers). Two key types of reactions are involved:

• Dehydration Reaction: A chemical reaction in which two molecules are covalently bonded to each other with the removal of a water molecule. This process synthesizes polymers from monomers.

• Hydrolysis: The reverse process, where a water molecule is added to break the bond between monomers, thus breaking down polymers into monomers.

Example: The formation of a peptide bond between two amino acids during protein synthesis is a dehydration reaction.

Proteins: Structure and Function

Overview of Proteins

Proteins are essential macromolecules composed of amino acid monomers. They perform a wide variety of functions in living organisms, including catalysis, transport, defense, and structural support.

• Monomer: Amino acid

• Polymer: Polypeptide (folds into a functional protein)

• Bond: Peptide bond (formed by dehydration reaction)

Functions of Proteins

• Enzymatic proteins: Catalyze biochemical reactions (e.g., digestive enzymes)

• Defensive proteins: Protect against disease (e.g., antibodies)

• Storage proteins: Store amino acids (e.g., casein in milk)

• Transport proteins: Transport substances (e.g., hemoglobin transports oxygen)

• Hormonal proteins: Coordinate organismal activities (e.g., insulin)

• Receptor proteins: Respond to chemical stimuli

• Contractile and motor proteins: Movement (e.g., actin and myosin in muscles)

• Structural proteins: Support (e.g., collagen in connective tissue)

Levels of Protein Structure

• Primary Structure: The unique sequence of amino acids in a polypeptide chain.

• Secondary Structure: Local folding of the polypeptide chain into structures such as alpha helices and beta-pleated sheets, stabilized by hydrogen bonds.

• Tertiary Structure: The overall three-dimensional shape of a polypeptide, resulting from interactions among side chains (R groups), including hydrophobic interactions, hydrogen bonds, ionic bonds, and disulfide bridges.

• Quaternary Structure: The association of two or more polypeptide subunits to form a functional protein.

Example: Hemoglobin is a quaternary protein composed of four polypeptide subunits.

Protein Denaturation

Protein structure is sensitive to environmental conditions. Changes in temperature, pH, or salt concentration can disrupt the weak interactions that maintain a protein's shape, causing denaturation (loss of native structure and function).

• Denaturation: The process by which a protein loses its shape and, therefore, its function due to the disruption of weak chemical bonds and interactions.

Energy in Biological Systems

Thermodynamics and Free Energy

Biological systems obey the laws of thermodynamics, which govern energy transformations.

• First Law of Thermodynamics: Energy cannot be created or destroyed, only transferred or transformed.

• Second Law of Thermodynamics: Every energy transfer increases the entropy (disorder) of the universe.

Free Energy (G): The portion of a system's energy that can perform work. Changes in free energy ($\Delta G$) determine whether a reaction is spontaneous.

• Exergonic Reaction: Releases energy; $\Delta G < 0$; spontaneous.

• Endergonic Reaction: Requires energy input; $\Delta G > 0$; non-spontaneous.

ATP: The Energy Currency of the Cell

Adenosine triphosphate (ATP) is the primary energy carrier in cells. Hydrolysis of ATP releases energy that can be used to drive endergonic reactions.

• ATP Hydrolysis: $\text{ATP} + \text{H}_2\text{O} \rightarrow \text{ADP} + \text{P}_i + \text{energy}$

• Energy Coupling: The use of exergonic processes (like ATP hydrolysis) to drive endergonic processes (such as muscle contraction or active transport).

Enzymes: Biological Catalysts

Enzyme Structure and Function

Enzymes are proteins that act as catalysts, speeding up chemical reactions by lowering the activation energy required for the reaction to proceed.

• Active Site: The region on the enzyme where the substrate binds and the reaction occurs.

• Substrate: The reactant molecule upon which an enzyme acts.

• Induced Fit Model: The enzyme changes shape slightly to fit the substrate more closely, facilitating the reaction.

Mechanisms of Enzyme Catalysis

• Orientation: Enzymes bring substrates together in the correct orientation to react.

• Straining Bonds: Enzymes apply stress to substrate bonds, making them easier to break.

• Providing a Favorable Microenvironment: The active site may provide optimal conditions (e.g., pH, charge) for the reaction.

• Covalent Catalysis: The enzyme may form a temporary covalent bond with the substrate.

Enzyme Activity and Environmental Effects

Enzyme activity can be affected by environmental factors such as temperature, pH, and the presence of inhibitors or activators. Extreme conditions can denature enzymes, reducing their activity.

Comparison of Exergonic and Endergonic Reactions

Property	Exergonic Reaction	Endergonic Reaction
Energy Change ($\Delta G$)	Negative ($\Delta G < 0$)	Positive ($\Delta G > 0$)
Spontaneity	Spontaneous	Non-spontaneous
Energy Flow	Energy released	Energy required
Example	Cellular respiration	Photosynthesis

Summary Table: Major Macromolecules in Cells

Macromolecule	Approximate % of Cell Mass	Function
Proteins	15%	Catalysis, structure, transport, defense, etc.
RNA	6%	Genetic information, protein synthesis
Polysaccharides	2%	Energy storage, structure
Phospholipids	2%	Membrane structure
DNA	1%	Genetic information
Small molecules & ions	4%	Various (signaling, metabolism, etc.)

Additional info: Some content and examples have been expanded for clarity and completeness based on standard General Biology curriculum.