chapter 2

Module 2: Chemistry of Life - Study Notes

Learning Objectives - Lesson 2.1

  • Describe the structure of an atom.
  • Define and discuss the terms element, molecule, and compound.
  • Compare and contrast the major types of chemical bonding.
  • Inorganic Chemistry:
    • Distinguish between organic and inorganic chemical compounds.
    • Discuss the chemical characteristics of water.
    • Discuss acids, bases, and salts.
    • Explain the concept of pH.
    • Discuss the structure and function of the following types of organic molecules:
    • Carbohydrate
    • Lipid
    • Protein
    • Nucleic Acid

Levels of Chemical Organization

  • Atom: Smallest unit of matter.
  • Nucleus: Central core of the atom.
  • Proton: Positively charged particle in the nucleus.
  • Neutron: Uncharged particle in the nucleus.
  • Atomic Number: Number of protons in the nucleus.
  • Atomic Mass: Number of protons and neutrons combined.

Atoms

  • Energy Levels: Orbital regions surrounding the atomic nucleus containing electrons.
  • Electron: Negatively charged particle.
    • Each energy level can contain up to eight electrons.
    • Energy level increases the farther it is from the nucleus.

Elements, Molecules, and Compounds

  • Element: A pure substance made up of only one kind of atom.
  • Molecule: A group of atoms bound together.
  • Compound: Substances whose molecules contain more than one kind of atom.

Chemical Bonding

  • Chemical bonds form to make atoms more stable.
  • Atoms react with one another to fill their outermost energy levels.
  • Atoms may share, donate, or borrow electrons to become stable.
Ionic Bonds
  • Ions form when an atom gains or loses electrons in its outer energy level.
    • An atom with one or two outer shell electrons may donate these electrons to become stable.
  • Positive Ion: An atom that has lost electrons, denoted by a superscript positive sign (e.g., Na+, Ca++).
  • Negative Ion: An atom that has gained electrons, denoted by a superscript negative sign (e.g., Cl−).
  • Ionic bonds form through the attraction of positive and negative ions.
  • Electrolyte: A molecule that dissociates in water to form individual ions; an ionic compound.
    • Many dissolved ions in the body plays important roles in muscle contraction, nerve signaling, and other vital functions.
Covalent Bonds
  • Covalent Bonds: Form when atoms share their outer energy ions to achieve stability.
  • Covalent bonds do not easily dissociate in water.
  • Used to form all major organic compounds in the body.
    • Atoms involved must remain close together, making covalent bonds not easily broken.
Hydrogen Bonds
  • Hydrogen Bonds:
    • Do not create new molecules; instead, they provide subtle forces that help large molecules maintain a specific shape.
    • Present in water, DNA, and proteins.

Quick Check Questions

  1. What are the three main subatomic particles of an atom?
  2. What is an ionic bond? What is a covalent bond?

Inorganic Chemistry

  • Organic Molecules: Contain carbon-carbon (C-C) and/or carbon-hydrogen (C-H) covalent bonds; inorganic molecules do not.
    • Few inorganic compounds contain carbon, and none have C-C or C-H bonds.
    • Organic molecules are generally larger and more complex than inorganic molecules.

Water

  • Water: An inorganic compound essential to life.
    • Functions as a solvent forming aqueous solutions in the body.
  • Involvement in chemical reactions including:
    • Dehydration Synthesis
    • Hydrolysis
  • Chemical reactions involve energy transfers, such as the energy used to build ATP molecules.
  • Chemical Equations show how reactants interact to form products, separated by arrows.

Acids, Bases, and Salts

  • Water molecules dissociate to form equal amounts of H+ (hydrogen ion) and OH− (hydroxide ion).
  • Acid: A substance that shifts the H+/OH− balance in favor of H+; produces an excess of H+ ions.
  • Base: A substance that shifts the H+/OH− balance against H+ (alkaline); produces an excess of OH−.
pH
  • pH: A mathematical expression of the relative H+ concentration in an aqueous solution.
    • A pH of 7 is neutral (neither acid nor base).
    • pH values > 7 are basic, while pH values < 7 are acidic.
pH (Cont.)
  • Neutralization occurs when acids and bases mix, forming salts.
  • Buffers: Chemical systems that absorb excess acids or bases to maintain a stable pH.
  • The pH of body fluids must be maintained within a narrow range of 7.35 - 7.45 to ensure normal body function.
  • Conditions like Acidosis and Alkalosis can be dangerous.
  • The body can eliminate excess H+ ions through urine or by increasing CO2 loss (an acid) via the respiratory system.

Organic Chemistry

Carbohydrates
  • Carbohydrates: Sugars and complex carbohydrates containing carbon (C), hydrogen (H), and oxygen (O).
    • Monosaccharides: Basic units of carbohydrate molecules (e.g., glucose, primary energy source for cells).
    • Disaccharide: Double sugar consisting of two monosaccharide units (e.g., sucrose, lactose).
    • Polysaccharide: Complex carbohydrates composed of multiple monosaccharide units (e.g., glycogen stored in the body).
    • Carbohydrates store potential energy in their bonds, releasing energy for work when broken.
Lipids: Fats and Oils
  • Triglycerides: Formed by one glycerol unit and three fatty acids, storing energy for later use.
    • Fatty acid components can be classified as saturated or unsaturated.
Phospholipids
  • Similar in structure to triglycerides but contain phosphorus units, having a hydrophilic head and two hydrophobic tails.
    • Form stable double layers (bilayers) in water, creating cell membranes.
Cholesterol
  • Molecules have a steroid structure, consisting of multiple rings.
    • Stabilizes phospholipid tails within cellular membranes and can be converted into steroid hormones.
Proteins
  • Very large molecules composed of amino acids linked in long, folded chains by peptide bonds.
    • All amino acids contain nitrogen (N).
    • Various amino acids are combined in specific sequences to form proteins.
    • Structural Proteins: Form essential body structures (e.g., collagen and keratin).
    • Functional Proteins: Participate in body chemistry (e.g., hormones, enzymes).
      • Enzymes: Catalysts facilitating chemical reactions; operate on a lock-and-key model where each enzyme fits specific substrate molecules.
Nucleic Acids
  • Composed of nucleotides, the building blocks of nucleic acids.
    • Each nucleotide contains a phosphate unit, a sugar (ribose or deoxyribose), and a nitrogen base (adenine, thymine, uracil, guanine, or cytosine).
Deoxyribonucleic Acid (DNA)
  • Serves as the cell's master code for protein assembly, utilizing deoxyribose sugar and bases A, T (not U), C, and G, forming a double helix structure.
Ribonucleic Acid (RNA)
  • Acts as a temporary working copy of a gene from the DNA, using ribose as the sugar and bases A, U (not T), C, and G.
Adenosine Triphosphate (ATP)
  • ATP is composed of adenine and three phosphate groups, with high-energy bonds.
    • Energy derived from nutrient breakdown is used for cellular processes.

Questions

  • Why is the structure of a protein molecule important?
  • What are enzymes and how do they function in the body?

Group Discussions

  • Scenario involving a sick child and the acidity of vomit.
  • Discussion about the implications of increasing hydrogen ion concentration in a solution.

Critical Thinking Case Study

  • Discussion on diabetic ketoacidosis and the potential dangers of acid balance in the bloodstream.

Group Activity

  • PH Lab Activity: Identify reactions and processes involved.

Questions?

  • Open floor for any questions regarding the chemistry of life topics covered in the module.