Alberts - Essential Cell Biology (4th ed.)

The Chemistry of Life

• Living creatures are complex chemical systems, exhibiting both diversity and intricate behaviors.

• The historical belief in a vital force (animus) that distinguishes living organisms has been debunked through scientific understanding, revealing that all biological entities adhere to chemical and physical laws.

Unique Aspects of Biochemical Chemistry

• Carbon Compounds: Organic chemistry, which focuses on carbon-based compounds, is fundamental to life. Carbon's unique ability to form stable bonds allows for the formation of diverse molecules necessary for life processes.

• Aqueous Solutions: Most biochemical reactions occur in aqueous environments, under specific temperature ranges that are finely tuned to the Earth's conditions, essential for sustaining life.

• Complexity: Even the simplest cellular structures demonstrate a complexity that surpasses the characteristics of conventional chemical systems, highlighting the sophisticated nature of biological functions.

• Polymeric Molecules: Fundamental cellular functions such as growth and reproduction are governed by large polymeric molecules, including proteins, nucleic acids, and polysaccharides, critical to life's processes.

• Regulation: Cells meticulously regulate their chemical reactions, determining not only the timing but also the spatial localization of reactions, ensuring efficiency and order in biological systems.

Fundamental Chemical Concepts

• Chemical Bonds: Matter consists of elements (like hydrogen and carbon), indivisible by chemical means.

  • Atoms: The building blocks of elements, with a nucleus containing positively charged protons and neutral neutrons, surrounded by negatively charged electrons.

  • Atomic Number: Represents the number of protons in an atom and defines its elemental identity; for instance, carbon (C) possesses six protons.

  • Isotopes: These are different variants of elements that have the same number of protons but differ in neutron count, maintaining identical chemical properties.

Molecular Weight and Moles

• Isotopes: Carbon-12 (12C) is stable, whereas Carbon-14 (14C) is radioactive, providing utility for dating organic materials.

• Atomic Weight: Calculated as the sum of protons and neutrons in an atom; molecular weights are typically expressed in daltons.

• Moles: One mole equates to approximately 6 × 10^23 molecules and is essential for quantitative chemistry calculations.

Elements in Living Systems

• Abundant Elements: The primary elements found in living organisms—carbon (C), hydrogen (H), oxygen (O), and nitrogen (N)—comprise about 96% of total body mass, underscoring their significance.

• The elemental composition in biological systems diverges appreciably from that of inorganic environments, which speaks to distinctive biochemical properties and interactions.

Electron Interaction and Bonding

• Electrons: The behavior and bonding capabilities of elements are determined predominantly by their outer (valence) electrons, which participate in the formation of chemical bonds.

• Covalent Bonds: Formed through the sharing of electrons between atoms, these are essential for creating stable molecules.

  • Single Bonds: Involve the sharing of one pair of electrons.

  • Double Bonds: Involve the sharing of two pairs of electrons.

• Polar Covalent Bonds: Characterized by unequal sharing of electrons, leading to the formation of partial positive and negative charges within molecules.

• Nonpolar Bonds: Involve the equal sharing of electrons, resulting in a neutral charge distribution.

Electron Shells and Reactivity

• Electron Shells: Electrons fill these shells in a sequential manner; atoms achieve stability when their outer shell is filled (e.g., noble gases).

• Atoms like carbon (C), nitrogen (N), and oxygen (O) with incomplete outer shells exhibit a tendency to react, engaging in various bonding types (ionic and covalent) to achieve full outer shells.

Types of Chemical Bonds

• Covalent Bonds: Characterized as the strongest type of bond due to the sharing of electrons, essential for stable molecular formation.

• Ionic Bonds: Created by the transfer of electrons from one atom to another, resulting in charged ions. For example, sodium (Na) loses an electron to form a Na+ ion, while chlorine (Cl) gains that electron to form a Cl-.

• Hydrogen Bonds: These are weak interactions, yet they are crucial for maintaining the structure of biological molecules, particularly in water and macromolecules.

• Van der Waals Attractions: These weak attractions arise from fluctuating electric charges and play significant roles in the interactions of macromolecules.

Molecules in Biological Processes

• Biological Molecules:

  • Small Organic Molecules: Essential building blocks like sugars, fatty acids, amino acids, and nucleotides are foundational to larger macromolecules.

    • Sugars: Function not only as energy sources but also as structural elements, with enzymes capable of interconverting them into various forms (e.g., glucose).

    • Fatty Acids: Non-polar and hydrophobic, these molecules are key in energy storage and the formation of cellular membranes.

    • Amino Acids: The basic units of proteins, linked by peptide bonds. The properties and functions of proteins are determined by the unique side chains of their constituent amino acids.

    • Nucleotides: The building blocks of nucleic acids (both DNA and RNA) that also serve energy-carrying functions (e.g., ATP) and are vital for genetic information storage and transfer.

• Macromolecules: These include proteins, nucleic acids, and polysaccharides, which are constructed from smaller units through covalent bonds and noncovalent interactions, which influence their shape and biological function.

Chemical Bonds Overview

• Bonds vary in strength: covalent bonds are the strongest, while hydrogen and ionic bonds are significantly weaker.

• Noncovalent bonds are vital for facilitating molecular recognition, stabilization of structures, and complex formation.

• A deep understanding of molecular interactions is crucial for comprehending cellular functions and the broader realm of biological chemistry.