Chapter 2

Chapter 2 - Physical Principles Underlying Cell Structure and Function

I. Chemical Composition of Cells

  • Overview of the chapter concerning the physical principles that underlie cell structure and function.

II. Properties of the Molecules Responsible for All Cellular Activities

  • The chapter examines the interactions and properties of chemical molecules that are fundamental for cellular activities.

III. Reminder from Chapter 1: Hierarchical Organization of Living Systems

  • Cellular Level:

    • Subatomic particles

    • Atoms

    • Molecules

    • Macromolecules

    • Organelles

    • Cells

  • Definition of a Cell:

    • The basic unit of life (known as Cell Theory).

Chapter 2.1: Focal Points: Chemical Bonds, Thermodynamics, and ATP

  • A. Atoms and Molecules Interact Through Chemical Bonds

    • Chemical bonds are the interactions that hold atoms together to form molecules.

  • B. The Laws of Thermodynamics and Free Energy Changes Govern Chemical Reactions

    • Thermodynamics describes the principles governing energy transformations.

  • C. Cells Use ATP as an Energy Source to Drive Energetically Unfavorable Reactions

    • ATP, or adenosine triphosphate, is critical for cellular energy transfer.

A. Chemical Bonds

  • Definition of Chemical Bonds:

    • Chemical bonds are forces that hold atoms together in molecules.

  • Types of Chemical Bonds:

    • Covalent Bonds:

    • Formed by the sharing of electrons between atoms, for instance between carbon and hydrogen.

    • Example: Covalent bond imagery illustrating the shared electrons.

    • Ionic Bonds:

    • Formed through the attraction between positively and negatively charged ions.

    • Example: Image showing ionic bond formation.

    • Hydrogen Bonds:

    • Weak attractions between polar molecules; essential in biological systems for creating complex structures like protein folds.

    • Example: Representation of hydrogen bonds in water and between amino acids in proteins.

    • Hydrophobic Interactions:

    • Occurs when nonpolar molecules aggregate to avoid contact with water, demonstrating the nature of molecular interactions in water-based environments.

B. Laws of Thermodynamics

  • First Law of Thermodynamics:

    • Energy cannot be created or destroyed, only transformed.

  • Second Law of Thermodynamics:

    • The total entropy of a system can never decrease over time; systems tend to move towards greater disorder.

  • Third Law of Thermodynamics:

    • As temperature approaches absolute zero, the entropy of a perfect crystal approaches zero.

C. ATP: Adenosine Triphosphate

  • Definition and Function:

    • ATP is the principal molecule for storing and transferring energy in cells.

    • Structure: Contains three phosphate groups; hydrolysis of these bonds releases energy.

    • High-Energy Bonds: The hydrolysis of these bonds results in a significant decrease in free energy enabling cellular processes.

Chapter 2.2: Organic Molecules of Cells

  • A. Carbohydrates

  • Definition:

    • Carbohydrates are biomolecules made of carbon, hydrogen, and oxygen.

    • Types of Carbohydrates:

    • Sugars:

      • Glucose is a simple six-carbon sugar
        to be used as a nutrient.

    • Starches:

      • Macromolecules composed of hundreds or thousands of sugars.

    • Fiber:

      • Indigestible by humans, assisting with digestive health.

  • Complex Carbohydrates:

    • Composed primarily of glucose residues.

    • Examples: Starch, glycogen, and cellulose.

  • B. Lipids

  • Definition:

    • Lipids are biomolecules primarily composed of fatty acids and glycerol.

    • Types of Lipids:

    • Fats:

      • Include triacylglycerols made of three fatty acids linked to glycerol.

    • Phospholipids:

      • Contain two fatty acids, a glycerol backbone, and a phosphate group, critical for cell membranes.

    • Sterols:

      • Include compounds like cholesterol.

  • C. Nucleic Acids

  • Definition:

    • Nucleic acids (DNA and RNA) comprise chains of nucleotides, serving as the genetic material.

    • Components of Nucleotides:

    • Composed of a sugar, a phosphate group, and a nitrogenous base.

    • DNA Structure:

    • Exists as a double helix held together by complementary base pairing: cytosine (C) pairs with guanine (G) and thymine (T) pairs with adenine (A).

  • D. Proteins

  • Definition:

    • Proteins are large macromolecules made from amino acids linked by peptide bonds and play various roles, including structural components and as enzymes.

    • Amino Acids Structure:

    • Each consists of a central carbon atom, an amino group, a carboxyl group, a hydrogen atom, and a side chain (R group).

  • Protein Structure Levels:

    • Primary: Sequence of amino acids

    • Secondary: Local folding (alpha helices and beta sheets)

    • Tertiary: Overall 3D shape

    • Quaternary: Complex of multiple protein subunits

  • Functions of Proteins:

    • Enzymatic activity, structural support, cell signaling, and immune responses.