Chemistry of Life Lecture Notes

Objective and Overview: The study of chemistry within the context of life involves understanding energy, hydrogen, reactions, electrons, molecules, and the universe. The material is based on "The Chemistry of Life" by Melanie M. Cooper and Michael W. Klymkowsky.
Key Topics Covered:
- 2.1 The Nature of Matter, Technology, and Biology.
- 2.2 Properties of Water.
- 2.3 Carbon.
- 2.4 Chemical Reactions.
Fundamental Concept: Atoms are the building blocks of everything on Earth. A common mnemonic/joke provided is: "Never trust an atom. They make up everything."
Visual Resource: TedEd provides a resource titled "Just how small is an atom?" to illustrate the scale of subatomic matter.

Atomic Composition: Atoms consist of three primary particles:
- Protons: Positively charged particles ( $+$ ).
- Neutrons: Neutral particles with no charge.
- Electrons: Negatively charged particles ( $-$ ).
Structural Organization:
- Nucleus: The central part of the atom containing both protons and neutrons.
- Electron Cloud: The space around the nucleus where electrons are located.
Specific Particle Characteristics:
- Protons: The number of protons determines the atomic number of an element. In a neutral atom, the number of protons equals the number of electrons.
- Neutrons: Along with protons, neutrons determine the atomic mass of an element.
- Electrons: These stay in orbitals around the nucleus. In neutral elements, the electron count is identical to the proton count.

Defining Elements: An element is a pure substance consisting entirely of one specific type of atom.
The Periodic Table: This is a system that organizes all known elements based on their atomic number. Each element is represented by a specific letter symbol.
Case Study: Helium ( $He$ ):
- Element Name: Helium.
- Atomic Number: $2$ .
- Protons: $2$ .
- Electrons: $2$ .
- Neutrons: $2$ .
Groups in the Periodic Table:
- Alkali metals, Alkaline earth metals, Transition metals, Post-transition metals, Metalloids, Other nonmetals, Halogens, Noble gases, Lanthanoids, and Actinoids.
- Specific examples shown include Calcium ( $Ca$ ) with atomic number $20$ and atomic mass $40.078$ , and Iron ( $Fe$ ) with atomic number $26$ and mass $55.85$ .

Isotopes: These are atoms of the same element that contain a different number of neutrons.
- While the number of neutrons varies, the number of protons must always stay the same for it to remain the same element; if the proton count changes, the element itself changes.
- Atomic Mass: The atomic mass displayed on the periodic table is the average weight of all naturally occurring isotopes of that element.
Radioactive Isotopes: These are specific isotopes that emit radioactive energy.
- They degrade at a consistent, fixed rate.
- Applications: They are used for dating organic materials and in various medical treatments.

Compounds: A chemical combination of two or more elements in definite proportions. Compounds are represented by a chemical formula.
- Example ( $NaCl$ ): One sodium atom and one chlorine atom.
- Example ( $H_2O$ ): Two hydrogen atoms and one oxygen atom.
Types of Chemical Bonds:
- Ionic Bonds: Involve the complete transfer of electrons from one atom to another, resulting in charged ions.
- Covalent Bonds: Involve the sharing of electrons between atoms.
- Van der Waals Forces: A type of attraction between molecules rather than a formal chemical bond.
- Metallic Bonds: Another type of bond characterized by a "sea" of shared electrons among metal atoms.

Polarity: Water is a polar molecule because there is an uneven distribution of charge.
- The "Ears" (Hydrogen atoms): These are positively charged ( $+$ ).
- The "Chin" (Oxygen atom): This is negatively charged ( $-$ ).
Hydrogen Bonds: Because of this polarity, the positive hydrogen side of one water molecule is attracted to the negative oxygen side of a different water molecule, forming a hydrogen bond.
Cohesion vs. Adhesion:
- Cohesion: Attraction between molecules of the same type. This creates surface tension in water.
- Adhesion: Attraction between different types of molecules. This is seen in the formation of a meniscus in a glass tube or water climbing a straw.

Mixtures: A material composed of two or more elements or compounds that are physically mixed together but are not chemically combined.
Solutions: A specific type of mixture where one substance dissolves into another.
- Solute: The substance that is being dissolved (e.g., Salt).
- Solvent: The substance doing the dissolving (e.g., Water, which is the solvent $90\%$ of the time).
- Salt Water Example: Solute = Salt; Solvent = Water.

pH Scale: A measurement system used to detect the concentration of acidic or basic levels in a substance. Maintaining stable pH levels is vital for homeostasis in the human body.
Logarithmic Nature: The pH scale is logarithmic, meaning each unit represents a tenfold change in concentration.
- Example: Soda with a $pH$ of $3.0$ is $1,000,000$ times more acidic than alkaline ionized water with a $pH$ of $9.0$ .
Health Standards:
- Human blood is slightly alkaline by design, with a specific target $pH$ of $7.365$ .
- Disease generally sets in at very dangerous acidic $pH$ levels.
- Medical claim: Cancer cells are reported to be unable to live in an alkaline environment above $pH$ of $8.3$ .

Ions: An atom that has lost or gained an electron, resulting in a charge.
- Cation: A positively charged ion (Mnemonic: "Cat-ion is pozzitively charged").
- Anion: A negatively charged ion.
Acids: Substances with a higher concentration of $H^+$ ions and a $pH$ lower than $7$ .
- Examples: Lemon juice, tomato juice, and Hydrochloric Acid ( $HCl$ ). $HCl$ is produced by the stomach for food digestion.
Bases (Alkaline): Substances with a high concentration of $OH^-$ ions and a $pH$ level above $7$ .
- Examples: Lye ( $NaOH$ ) used in soap making, oven cleaner, and bleach.
Buffers: These are weak acids or bases that react with strong acids or bases to prevent sharp, sudden changes in $pH$ . They are essential for maintaining the body's internal homeostasis.

Metabolic Impact Notice: The direct $pH$ of a food does not always match its metabolic impact on the body.
- Example: Lemons and limes are chemically acidic but have an alkalizing effect once metabolized.
- Example: Meats often test as alkaline when undigested but release acids into the body after consumption.
Categorization of Substances:
- Highly Acidic ( $pH$ 3.0-5.0): Colas ( $pH$ 2.5), bacon, processed cheeses, French fries, pudding, alcohol, white vinegar, and cigarettes.
- Neutral to Mildly Acidic ( $pH$ 6.0-7.0): Tap water, fruit juices, most whole grain breads, eggs, liver, and pharmaceutical drugs.
- Highly Alkaline ( $pH$ 8.0-10.0): Alkaline water ( $pH$ 9.0-10.0), baking soda, fresh lemon, raw spinach, raw kale, raw broccoli, and wheat grass.