Chapter 2

Chapter 2 – The Chemistry of Life

Overview of Atoms

  • Atoms: The basic units of matter

    • Depicted in Figure 2.2

  • Composed of three subatomic particles:

    • Protons: Positively charged particles.

    • Neutrons: Neutral particles with no charge.

    • Electrons: Negatively charged particles that orbit the nucleus.

  • Isotopes: Variants of a given element with the same number of protons but a different number of neutrons.

  • Radioactive decay: Occurs when an atom breaks up.

  • The chemical nature of an atom is determined by the mass and number of its electrons.

Structure of Atoms

  • Definition of an Atom: The smallest unit of an element that retains its physical and chemical properties.

  • Molecules: Formed when atoms bond together.

Subatomic Particles

  • Neutrons: Neutral particles within the nucleus.

  • Protons: Positively charged particles within the nucleus.

  • Electrons: Negatively charged particles that orbit around the nucleus.

Properties of Atoms

  • Atoms contain

    • Nucleus: Contains protons and neutrons.

    • Electron shells: Levels of energy where electrons reside.

  • Atomic number: The number of protons in an atom, unique to each element.

  • Mass number: The total number of protons and neutrons in the nucleus.

    • Each proton and neutron has a mass approximately equal to 1 atomic mass unit (AMU).

    • Electrons have negligible mass.

  • Atomic mass: The average mass of an atom reflecting the mass of isotopes.

Composition of Select Elements




  • Table of Common Elements in Living Organisms:


    Element

    Symbol

    Atomic Number

    Mass Number



    Hydrogen

    H

    1

    1.008



    Carbon

    C

    6

    12.011



    Nitrogen

    N

    7

    14.007



    Oxygen

    O

    8

    15.999



    Sodium

    Na

    11

    22.989



    Magnesium

    Mg

    12

    24.305



    Phosphorus

    P

    15

    30.974



    Sulfur

    S

    16

    32.064



    Potassium

    K

    19

    39.098



    Iron

    Fe

    26

    55.847



    Iodine

    I

    53

    126.904







    Atomic Structure





    • The majority of living organisms consist mainly of:

      • Oxygen, Carbon, Hydrogen, and Nitrogen.

    • Other important elements: Calcium, Phosphorus, Sulfur, Sodium, Chlorine, Magnesium, along with trace elements such as Iron, Iodine, and Selenium.

    • Total of 91 naturally occurring elements; only 24 are found in the human body.

    Electrons and Energy Levels

    • Electrons possess energy and move in electron shells.

    • The number of electrons corresponds with the number of protons in neutral atoms.

      • The innermost energy shell can hold a maximum of 2 electrons, while subsequent shells can hold up to 8 electrons.

    • Atoms energetically favor having full valence shells, leading to them being more stable when outer shells (valence shells) are filled.

    Electron Shell Configuration

    • Electrons fill energy shells from the innermost to the outermost, with the outermost electrons referred to as valence electrons.

    Chemical Bonds and Interactions

    • Molecules: The smallest unit of a substance that retains all chemical properties.

    • Compounds: Substances composed of two or more different types of atoms bonded together through various types of chemical bonds:

      • Covalent bonds: Atoms share electrons to fill their valence shells. Each atom contributes one electron to the shared pair.

      • Ionic bonds: Formed when one atom transfers electrons to another, creating oppositely charged ions that attract each other.

      • Hydrogen bonds: Weaker interactions that occur, for example, when hydrogen is bonded to electronegative elements like oxygen or nitrogen, resulting in polar molecules.

    Types of Chemical Bonds

    • 1. Ionic Bonds: Result from the transfer of electrons from one atom to another, leading to the formation of charged ions which are then attracted to each other due to their opposite charges.

    • 2. Covalent Bonds: Couples the sharing of electrons between atoms, which allows each paralleled atom to achieve a stable electron configuration.

    • 3. Hydrogen Bonds: Weak but crucial bonds that contribute to molecular structures and stability in biological molecules, especially water.

    Properties of Water

    • Water's unique properties make it vital for life due to its hydrogen bonding:

      • High Specific Heat: Requires significant energy to increase temperature, stabilizing cell environments.

      • High Heat of Vaporization: Substantial energy is required to convert water from liquid to gas.

      • Cohesion and Adhesion: Water molecules are unique in their affinity for each other (cohesion) and to other substances (adhesion), contributing to surface tension and molecular interactions.

      • Solvent Properties: Water can dissolve a variety of substances, a capability that is critical for biochemical reactions.

      • pH and Ionization: Water ionizes to yield H+ and OH- ions, where pH measures H+ concentration. ACIDS add H+ ions, while BASES remove H+ or add OH- ions.

      • Buffers: Compounds that maintain pH stability by balancing the addition or removal of acids and bases.

    Macromolecules in Living Organisms

    • Macromolecules are essential components, primarily made up of smaller subunits, or functional groups.

    • Four Main Classes of Macromolecules:

      • Proteins: Composed of amino acids; perform functions like structure, enzymes, transport, and defense.

      • Nucleic Acids: Composed of nucleotides; include DNA and RNA, critical for genetic information and protein synthesis.

      • Carbohydrates: Composed of sugar monomers like glucose, important for energy release and support in cells.

      • Lipids: Hydrophobic molecules, including triglycerides, phospholipids, and steroids, serve in energy storage and cellular structure.

    Polymer Formation and Breakdown

    • Two key processes for macromolecules:

      • Dehydration Synthesis: Joins monomer units by removing water to form bonds.

      • Hydrolysis: Breaks down polymers by adding water to disrupt bonds.

    Proteins and Their Structure

    • Protein Structures:

      • Primary: Sequence of amino acids.

      • Secondary: Coiling or pleating due to hydrogen bonds.

      • Tertiary: Overall 3D structure of a single polypeptide.

      • Quaternary: Combination of multiple polypeptides.

    • Denaturation: A process that unfolds proteins resulting in loss of function.

    Nucleic Acids

    • DNA and RNA: Key components for genetic information and synthesis of proteins.

    • Differences between DNA and RNA:

      • Structure: DNA is double-stranded, while RNA is single-stranded.

      • Bases: DNA contains thymine while RNA contains uracil.

      • Sugar: DNA contains deoxyribose, while RNA contains ribose.

    Adenosine Triphosphate (ATP)

    • Recognized as the energy currency of the cell, facilitating energy transfer during chemical reactions.

    Carbohydrates

    • Composition: Consist of C, H, and O in a 1:2:1 ratio.

      • Monosaccharides: Simple sugars (e.g., glucose).

      • Disaccharides: Composed of two monosaccharides (e.g., sucrose).

      • Polysaccharides: Long chains of monosaccharides (e.g., starch, glycogen).

    Lipids

    • Hydrophobic molecules primarily made of long-chain fatty acids.

    • Types of lipids and functions include:

      • Triglycerides: Energy storage molecules composed of three fatty acids attached to glycerol.

      • Phospholipids: Key components of cellular membranes with hydrophobic tails and hydrophilic heads.

      • Steroids: Function in signaling and as structural components in membranes.

    Summary of Macromolecules

    • Identifying major groups of macromolecules and their sub-groups/functions.

    • Compare dehydration synthesis with hydrolysis for metabolism of macromolecules.