General Biology Study Notes: Polysaccharides, Protein Structure, and Metabolism

Polysaccharides in Plants

Starch and Cellulose

Plants produce several types of polysaccharides, with starch and cellulose being two of the most important. These molecules serve different functions and have distinct structural properties.

• Starch: The primary storage form of glucose in plants. It is composed of two types of molecules: amylose (unbranched) and amylopectin (somewhat branched).

• Cellulose: A structural polysaccharide that forms the main component of plant cell walls. It consists of unbranched chains of glucose molecules.

• Key Difference: Starch is used for energy storage, while cellulose provides structural support.

• Branching: Starch (especially amylopectin) is more branched than cellulose, which is unbranched. The statement "Cellulose tends to be more branched than starch" is false.

• Hydrolysis: Plants can break down starch into glucose monomers via hydrolysis when energy is needed.

• Hydrogen Bonding: Cellulose molecules can form hydrogen bonds with each other, contributing to the rigidity of plant cell walls.

Example: Potato tubers store starch in plastids, while the rigid structure of a tree trunk is due to cellulose in the cell walls.

Protein Structure

Secondary Structure and the Polypeptide Backbone

Proteins are polymers of amino acids that fold into specific three-dimensional structures. The secondary structure of a protein refers to local folding patterns stabilized by hydrogen bonds.

• Polypeptide Backbone: The hydrogen bonds that stabilize secondary structures (such as alpha helices and beta pleated sheets) form between atoms of the polypeptide backbone, not the side chains.

• Alpha Helix: A coiled structure stabilized by hydrogen bonds between every fourth amino acid.

• Beta Pleated Sheet: Sheet-like structures formed by hydrogen bonds between parallel or antiparallel strands of the polypeptide backbone.

• Side Chains: While important for tertiary structure, side chains do not participate directly in the hydrogen bonds that define secondary structure.

Example: The fibrous protein keratin in hair and nails is rich in alpha helices, while silk fibroin is composed mainly of beta sheets.

Metabolism Overview

Definition and Pathways

Metabolism is the sum of all chemical reactions occurring within an organism. These reactions are organized into metabolic pathways, where each step is catalyzed by a specific enzyme.

• Anabolism: Energy-requiring pathways that build complex molecules from simpler ones (e.g., protein synthesis from amino acids).

• Catabolism: Energy-releasing pathways that break down complex molecules into simpler ones (e.g., cellular respiration).

• Metabolic Pathway: A series of enzyme-catalyzed reactions that transform a specific molecule into a product.

Example: The breakdown of glucose during cellular respiration is a catabolic pathway, while the synthesis of DNA is anabolic.

Energy and Thermodynamics in Biology

Types of Energy

Energy is the capacity to do work or cause change. In biological systems, energy exists in various forms:

• Kinetic Energy: Energy of motion (e.g., movement of molecules).

• Thermal Energy: Kinetic energy associated with the random movement of atoms or molecules; transferred as heat.

• Potential Energy: Stored energy due to position or structure (e.g., chemical bonds).

• Chemical Energy: A form of potential energy stored in chemical bonds, released during chemical reactions.

Thermodynamics and Free Energy

Biological systems obey the laws of thermodynamics:

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

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

The free-energy change ($\Delta G$) of a reaction determines whether it occurs spontaneously:

• $\Delta G < 0$: Spontaneous (exergonic) reaction; energy is released.

• $\Delta G > 0$: Nonspontaneous (endergonic) reaction; energy is required.

• $\Delta G = 0$: System is at equilibrium.

Equation:

$\Delta G = \Delta H - T\Delta S$

where $\Delta H$ is the change in enthalpy, $T$ is temperature in Kelvin, and $\Delta S$ is the change in entropy.

ATP and Energy Coupling

ATP Structure and Function

Adenosine triphosphate (ATP) is the primary energy currency of the cell. It consists of an adenine base, a ribose sugar, and three phosphate groups.

• Hydrolysis of ATP: Releases energy by breaking the terminal phosphate bond:

$\text{ATP} + \text{H}_2\text{O} \rightarrow \text{ADP} + \text{P}_i$

$\Delta G = -7.3$ kcal/mol

• Regeneration: ATP is regenerated from ADP and inorganic phosphate using energy from catabolic reactions:

$\text{ADP} + \text{P}_i \rightarrow \text{ATP}$

$\Delta G = +7.3$ kcal/mol

Energy Coupling

Cells use energy coupling to drive endergonic (energy-consuming) reactions by pairing them with exergonic (energy-releasing) reactions, often using ATP as the intermediary.

• Chemical Work: Driving endergonic reactions (e.g., synthesis of macromolecules).

• Transport Work: Pumping substances across membranes against their concentration gradient.

• Mechanical Work: Movement, such as muscle contraction or movement of vesicles along cytoskeletal tracks.

Enzymes and Metabolic Reactions

Enzyme Function and Specificity

Enzymes are biological catalysts that speed up chemical reactions by lowering the activation energy ($E_A$) required for the reaction to proceed.

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

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

• Enzyme-Substrate Complex: Temporary association between enzyme and substrate during the reaction.

• Specificity: Each enzyme is specific to its substrate due to the unique shape of its active site.

Example: The enzyme sucrase catalyzes the hydrolysis of sucrose into glucose and fructose.

Factors Affecting Enzyme Activity

Enzyme activity can be influenced by several factors:

• Temperature: Each enzyme has an optimal temperature at which it functions most efficiently. Too high or too low temperatures can denature the enzyme or slow the reaction.

• pH: Each enzyme also has an optimal pH range.

• Chemicals: Certain chemicals can inhibit or enhance enzyme activity.

Example: Human enzymes typically have an optimal temperature around 37°C, while enzymes from thermophilic bacteria may function best at much higher temperatures.

Summary Table: Comparison of Starch and Cellulose

Property	Starch	Cellulose
Function	Energy storage	Structural support
Branching	Branched (amylopectin) and unbranched (amylose)	Unbranched
Monomer	Glucose	Glucose
Location	Plastids (e.g., potato tubers)	Cell walls
Hydrogen Bonding	Minimal between chains	Extensive between chains