Study Notes on the Chemistry of Life and Atomic Structure

Necessity of Chemistry Knowledge: To truly understand biology, a foundational knowledge of chemistry is required because biological systems are built upon chemical principles.
Definition of Chemistry: Chemistry is defined as the study of matter.
Definition of Matter: * Matter is the composition of everything that makes up the entire universe, encompassing both living and non-living things. * This includes humans, galaxies, and all entities in between. * At the most fundamental level, matter is composed of atoms.

Composition: Matter is made up of quadrillions of atoms.
Functional Arrangement: Atoms arrange themselves in specific ways to create specific functions.
The Carbon Comparison: * Humans are essentially a buildup of atoms (primarily carbon) arranged in a specific way that enables life, thought, and communication. * A rock is also made of carbon, but because its carbon atoms are arranged differently, it cannot think or perform actions like listening to "Spotify Top 50."
The Basic Unit: * In biology and general chemistry, an atom (or element) is considered the base unit of matter that cannot be broken down into anything smaller. * Physicist Perspective: From the perspective of a physicist, atoms can be broken down further into subatomic particles called quarks. However, for biological study, the atom remains the functional basic unit.

The Human Analogy: * Atoms: Can be thought of as the category "human." * Elements: Can be thought of as specific individual names or personalities within that category.
Defining Elements: An element is a specific atom given a certain set of characteristics.
Examples of Elements: Carbon, Oxygen, Nitrogen, Uranium, Palladium, Gold, Silver, and Copper are all atoms, but they are distinct elements with unique properties and behaviors.

Internal Composition: Every atom is composed of three basic subatomic particles: protons, neutrons, and electrons.
The Nucleus: Found at the interior of the atom, the nucleus contains: * Protons: Positively charged particles ( $+$ ). * Neutrons: Neutrally charged particles (no charge).
The Electron Orbit: Electrons carry a negative charge ( $-$ ) and spin at "lightning speed" around the nucleus. * This is often compared to planets orbiting a sun. * Electromagnetic Attraction: The positive charge of the protons in the nucleus keeps the negatively charged electrons in check and prevents them from pulling away, ensuring they stay in the vicinity of the atom.
States of Existence: * Few atoms exist independently. * Most atoms are bound to other atoms to form molecules and compounds, such as water, proteins, or carbohydrates.
Delicacy and Stability: The balance of an atom is delicate. For example, in a uranium atom used in a nuclear bomb, removing a single electron can cause it to become unstable and explode, potentially destroying $10$ to $15$ miles of civilization.

The Atomic Number: This is the primary way to define an element. It represents the number of protons in the atom's nucleus. * The atomic number is usually displayed at the top of an element's entry on the periodic table. * Examples: * Hydrogen: $1$ * Lithium: $3$ * Carbon: $6$ * Nitrogen: $7$ * Oxygen: $8$ * Sodium: $11$
Atomic Mass: This is defined as the sum of the protons and the neutrons in the nucleus. * $\text{Atomic Mass} = \text{Protons} + \text{Neutrons}$ * Calculations: If the atomic mass and the atomic number (protons) are known, the number of neutrons can be calculated by subtraction ( $\text{Mass} - \text{Protons} = \text{Neutrons}$ ).
Rounding Rule: In this biology context (as opposed to a strict chemistry class), atomic masses are rounded to the nearest whole number. For example, Lithium's mass of $6.941$ is rounded to $7$ .
Invariance of Protons: The number of protons in an element does not change. If the proton number changes, the element itself changes into a different element with different behaviors. While this can happen in nature (radioactive decay), for standard biological study, the proton number is considered fixed.

Definition of Isotopes: Isotopes are versions of the same element that have the same number of protons but different numbers of neutrons. This gives them different atomic weights.
The Average Mass: The decimal numbers seen on the periodic table (e.g., $12.9277$ ) represent the average mass of all naturally occurring isotopes of that element based on their abundance.
Carbon Isotopes: * Carbon-12: The standard form ( $6$ protons, $6$ neutrons). * Carbon-13: Contains $7$ neutrons. * Carbon-14: Contains $8$ neutrons.
Conservation of Matter: The total amount of carbon in the universe remains constant; it is recycled through processes like photosynthesis and the carbon cycle. The number of carbon atoms today will be the same in $10,000,000$ years.

Fossil Dating: Carbon-14 is used to measure the age of fossils. It decays back into Carbon-12 at a known rate (e.g., half of Carbon-14 decays every $6,000$ years). By tracking the remaining Carbon-14 in a specimen, scientists can determine how many thousands of years have passed since the organism was buried.
Medical Imaging: Technologies like X-rays, CT scans, and MRIs harness the power of radioactive isotope decay. The energy released as electrons or neutrons decay allows for the visualization of internal structures.
Measuring Atomic Mass: Scientists use machines to move compounds at the speed of light to capture images and calculate mass. While the Large Hadron Collider is a well-known example of high-speed particle acceleration for other purposes, similar concepts are used to determine AMUs.
Atomic Mass Units (AMU): This is the specific unit of measurement for atomic mass, distinct from grams or pounds, though they can be converted to grams in chemistry.
Nutritional Science: Similar chemical processes were used to define and calculate the calorie.

Student Question: How many neutrons are in Oxygen if it has an atomic number of $6$ and a mass of $12$ ?
Speaker Correction: The speaker initially uses those numbers for oxygen as a hypothetical but corrects them: Carbon has an atomic number of $6$ and a mass of $12$ (resulting in $6$ neutrons). Oxygen actually has an atomic number of $8$ .
Example Calculation (Nitrogen): Nitrogen has an atomic mass of roughly $14$ and $7$ protons. This means it has $7$ neutrons ( $14 - 7 = 7$ ).
Session Conclusion: The class ended for a break at $6:07$ PM, with instructions to return at $6:15$ PM.