Atoms and Chemistry Notes

Atoms and Chemistry

Biology is the science of life, but life and non-life are made of substances studied in chemistry. Organisms are chemical machines, making chemistry essential in biology.

Matter and Atoms

Matter is any substance with mass occupying space. All matter consists of atoms, the smallest unit of a substance that retains its chemical properties. Each atom contains:

  • A nucleus with protons (positive charge) and neutrons (no charge).
  • Electrons (negative charge) orbiting the nucleus.

In a neutral atom, the number of electrons equals the number of protons.

Mass vs. Weight:

  • Mass: the amount of a substance.
  • Weight: the force of gravity on a substance.

An object's mass remains constant, but weight varies with gravity.

Atomic Number and Mass Number

  • Atomic number: the number of protons in the nucleus; determines the element.
  • Element: A substance that cannot be broken down chemically into other substances.
  • Mass number: the total number of protons and neutrons in the nucleus.

Electrons have negligible mass (approximately 1/1840 the mass of a proton), but they dictate chemical behavior.

Electrons and Energy

Electrons are attracted to the nucleus but repel each other. Maintaining their orbit requires work, giving them potential energy. Moving an electron:

  • Farther from the nucleus: requires energy, increases potential energy.
  • Closer to the nucleus: releases energy, decreases potential energy.

Cells use the potential energy of electrons to drive chemical reactions.

Electron Shells and Orbitals:

  • Electrons occupy energy levels called electron shells, with complex 3D shapes.
  • Orbitals are volumes of space where electrons are most likely to be found; each contains up to two electrons.
  • The first shell has one spherical s orbital.
  • Subsequent shells have four p orbitals (dumbbell-shaped) and hold up to eight electrons.

Atoms react to fill their outermost electron shell by losing, gaining, or sharing electrons, forming chemical bonds.

Ions and Isotopes

Ions

Ions are atoms with an unequal number of protons and electrons (charged).

  • Cations: positively charged ions (lose electrons).
    Na
    Rightarrow Na^+ + e^-
  • Anions: negatively charged ions (gain electrons).
    Cl + e^-
    Rightarrow Cl^-

Isotopes

Isotopes are atoms with the same number of protons but different numbers of neutrons.

  • They have the same atomic number but different mass numbers.
  • For example, carbon has isotopes like carbon-12 (^{12}C) and carbon-14 (^{14}C).

Radioactive Isotopes

Radioactive isotopes have unstable nuclei that decay, emitting particles with lower atomic numbers. Radioactive isotopes are useful in medicine as tracers and in dating fossils.

Example: PET and PET CT imaging to detect cancerous areas.

Dating Fossils with Carbon-14

A fossil is any record of prehistoric life (older than 10,000 years). Radiocarbon dating uses the decay of carbon-14 (^{14}C) to date fossils up to 50,000 years old. $^{14}C$ is created by cosmic rays interacting with nitrogen-14 (^{14}N$).

  • Plants capture ^{14}C during photosynthesis, and animals acquire it by eating plants.
  • After death, ^{14}C decays back to ^{14}N, while ^{12}C remains constant.
  • The ratio of ^{14}C to ^{12}C indicates the time elapsed since death.
  • Half-life: the time for half of the radioactive isotope to decay.

Carbon-14 has a half-life of 5,730 years.

Nt = N0 \, (1/2)^{(t / t_{1/2})}

Where:

  • N_t is the amount of the substance remaining after time t.
  • N_0 is the initial amount of the substance.
  • t is the time elapsed.
  • t_{1/2} is the half-life of the substance.

For fossils older than 50,000 years, scientists use isotopes like potassium-40 (^{40}K), which decays into argon-40 (^{40}Ar) with a half-life of 1.3 billion years.

Molecules and Chemical Bonds

A molecule is a group of atoms held together by energy in chemical bonds. There are three primary types:

Ionic Bonds

Ionic bonds result from the attraction between oppositely charged ions. For instance, table salt (NaCl) is formed through ionic bonds.

Covalent Bonds

Covalent bonds involve the SHARING of electrons between atoms to fill their outermost shells, forming single, double, or triple bonds.

Atoms like hydrogen (H) form one covalent bond, while carbon (C), nitrogen (N), and oxygen (O) form multiple. The carbon atom has four electrons in its outermost shell, so carbon can form as many as four covalent bonds in its attempt to fully populate its outermost shell of electrons, allowing them to participate in various molecules.

Energy and Covalent Bonds

Breaking covalent bonds releases energy (e.g., the Hindenburg explosion involving H_2).

Electronegativity: an atom's ability to attract shared electrons. It determines if a covalent bond is:

  • Polar: unequal sharing of electrons, creating partial charges (e.g., water).
  • Nonpolar: equal sharing of electrons (e.g., methane).

Covalent bonds are strong and directional, making them ideal for building molecules.

Hydrogen Bonds

Hydrogen bonds are weak bonds between polar molecules like water, where the positive end of one molecule attracts the negative end of another (electropositive hydrogen to electronegative oxygen or nitrogen).

They are weak individually but collectively strong, like Velcro. They are highly directional and crucial in biological molecules, (e.g., protein and DNA structure).

Van Der Waals Forces

Van der Waals forces are weak, non-directional attractions between atoms when very close. They are significant when numerous atoms are in proximity, such as antibody-virus recognition.

Water: Cradle of Life

Water (H2O) covers three-fourths of Earth and makes up two-thirds of the human body. Its properties are due to its polarity and hydrogen bonds.

Properties of Water

  1. Heat Storage: Water heats up slowly and retains heat due to hydrogen bonds.
  2. Ice Formation: Ice is less dense than water because stable hydrogen bonds hold molecules farther apart.
  3. High Heat of Vaporization: Evaporation requires much heat energy, cooling surfaces (e.g., sweating).
  4. Cohesion: Attraction between water molecules creates surface tension.
  5. Adhesion: Attraction between water and other polar molecules causes capillary action.
  6. Polarity: Water is an excellent solvent for polar molecules (hydrophilic) due to hydrogen bond formation and hydration shells. Nonpolar molecules (hydrophobic) cluster together in water.

Water Ionization and pH

Water molecules spontaneously ionize, forming hydrogen ions (H^+) and hydroxide ions (OH^-). This ionization is rare (1 in 550 million molecules).

pH Scale: measures hydrogen ion concentration on a negative logarithmic scale:

pH = -log[H^+]

  • pH 7: Neutral ([H^+] = [OH^-])
  • pH < 7: Acidic (excess of H^+)
  • pH > 7: Basic (excess of OH^-)

A difference of one pH unit represents a tenfold change in H^+ concentration.

Acids: Substances that increase H^+ concentration.

Bases: Substances that decrease H^+ concentration.

Acid Rain

Acid rain is caused by pollutants like sulfur dioxide (SO2) from coal-burning plants, which form sulfuric acid (H2SO_4) in the atmosphere. This acid rain damages ecosystems by acidifying soils and lakes.

Buffers

Buffers minimize pH changes by absorbing or releasing H^+.

The key buffer in human blood is the carbonic acid and bicarbonate pair:

CO2 + H2O \rightleftharpoons H2CO3 \rightleftharpoons HCO_3^- + H^+

This system stabilizes blood pH and is affected by breathing (CO2 levels).

Case Study: Otzi the Iceman

Otzi, a corpse found in the Alps, was dated using carbon-14 dating. By measuring the ratio of ^{14}C to ^{12}C$$, scientists determined Otzi lived approximately 5,300 years ago.

Fukushima Nuclear Accident

Nuclear power plants use radioactive isotopes like uranium-235, which undergo fission and release tremendous heat. Water is used to absorb this heat to generate steam and create electricity.

The Fukushima accident occurred after an earthquake and tsunami disabled cooling systems, leading to hydrogen gas explosions and radioactive release. The accident was caused by a loss of water circulation around the uranium rods as a means to absorb the heat generated by the nuclear reactors.

Questions

  • Why don't carbon atoms (four valence electrons) form a diatomic gas like hydrogen, oxygen, and nitrogen?
  • Why do scientists look for water as an indication of life over other molecules?