Life Sciences: Basic Chemistry and Atomic Structure

Overview of Matter and Its States

• Definition of Matter: Matter is used to describe objects that occupy space and possess a discernible mass.

• Relationship to Life Sciences: At the most basic level of organization, the human body is found at the chemical level. All cells, tissues, and organs are comprised of matter.

• States of Matter: Matter exists in three major states: solid, liquid, and gas. A substance may change from one state to another through heating and cooling. When a material changes state, its smallest units, called molecules, behave differently.

Solids

• Structure: Atoms are arranged in fixed positions with a definite shape and volume.

• Kinetic Energy: Solids have the lowest amount of kinetic energy among the three states.

• Intermolecular Forces: Strong intermolecular forces between atoms prevent them from moving freely; instead, they vibrate constantly.

• Example: Bone.

Liquids

• Structure: Liquids have a constant volume but do not take a definite shape; they assume the shape of their container.

• Kinetic Energy: They possess more kinetic energy than solids.

• Intermolecular Forces: The forces between atoms are weaker than in solids, allowing for limited movement within the confines of the container.

• Examples: Blood plasma and water.

Gases

• Structure: Gases have neither a definite shape nor a definite volume.

• Kinetic Energy: Gases contain the highest amount of kinetic energy.

• Intermolecular Forces: Intermolecular forces are much weaker, creating large spaces between gaseous molecules and allowing them to move freely.

• Examples: Oxygen and Nitrogen.

The Atom: Basic Building Block of Chemistry

• Definition: An atom is the basic building block of chemistry. It is the smallest unit into which matter can be divided without the release of electrically charged particles.

• Role in Biology: Understanding atomic structure is critical for understanding the nature of biological molecules and other molecules interacting with biological systems.

• Subatomic Particles:

  • Proton ($p^+$): Positively charged particles located in the Nucleus.

  • Neutron ($n^0$): Neutral particles located in the Nucleus.

  • Electron ($e^-$): Negatively charged particles that occupy the space around the nucleus in orbitals.

Models and Electron Configuration

• Evolution of Models: Atomic models evolve over time as new instrumentation becomes available and understanding is refined.

• Bohr Model: Electrons are considered to be orbiting around the nucleus in discrete shells or orbits (energy levels) at specific distances. They are maintained in orbit by their attraction to positive protons.

• Electron Shell Capacities:

  • First Energy Level: $2$ electrons.

  • Second Energy Level: $8$ electrons.

  • Third Energy Level: $18$ electrons.

  • Fourth Energy Level: $32$ electrons.

Electron Shell Examples (Atomic Number Order)

• Hydrogen ($1$)

• Helium ($2$)

• Lithium ($2, 1$)

• Beryllium ($2, 2$)

• Boron ($2, 3$)

• Carbon ($2, 4$)

• Nitrogen ($2, 5$)

• Oxygen ($2, 6$)

• Fluorine ($2, 7$)

• Neon ($2, 8$)

Atomic Number and Atomic Mass

• Atomic Number: An atom is defined by the number of protons ($p^+$) in its nucleus. Since an atom is electrically neutral, for every $p^+$ there is one $e^-$.

  • $\text{Atomic number} = \text{number of } p^+$

• Atomic Mass: Determined primarily by the presence of protons and neutrons. Electrons have negligible mass.

  • $\text{Atomic mass} = \text{number of } p^+ + \text{number of } n^0$

• Units (Daltons): Mass is measured in units called Daltons ($Da$).

  • Proton: $1\,Da$

  • Neutron: $1\,Da$

  • Electron: $1/1840\,Da$

• Example: One carbon atom with $6$ protons and $6$ neutrons has an atomic mass of:

  • $6\,Da + 6\,Da = 12.00\,Da$

Ions and Charge

• Definition: Atoms in which the number of electrons does not equal the number of protons are called ions; they possess an overall charge.

• Cation: A positively charged ion formed when an atom loses electrons.

  • Example: Sodium ($Na$) loses one electron: $Na \rightarrow Na^+ + e^-$

• Anion: A negatively charged ion formed when an atom gains electrons.

  • Example: Chlorine ($Cl$) gains one electron: $Cl + e^- \rightarrow Cl^-$

Isotopes and Radioactivity

• Definition: Isotopes are forms of the same element that contain equal numbers of protons but different numbers of neutrons in their nuclei. Consequently, they differ in relative atomic mass but not in chemical properties.

• Natural Occurrence: Elements often exist in nature as mixtures of isotopes.

  • Carbon Isotopes:

    • $C-12$: Most abundant ($98.9\%$)

    • $C-13$: $1.1\%$

    • $C-14$: <0.0001\%

• Radioactive Decay: Extra neutrons can make a nucleus unstable or "bulky." When the nucleus breaks apart, it generates elements with lower atomic numbers, radiation (particles), and high energy release.

• Half-life: Nuclei decay at different but constant rates.

• Applications:

  • Carbon-14 dating: Used for historical dating ($t_{1/2} = 5,730$ years).

  • Nuclear medicine: Diagnostic tools (tracers) using radioisotope-tagged molecules.

  • Radiotherapy: Used as a therapeutic tool.

Molecule, Element, and Compound

• Molecule: A chemical structure held together by shared electrons (e.g., $O_2$).

• Element: A pure substance consisting only of atoms that have the same number of protons. They cannot be broken down into simpler substances by chemical reactions.

• Compound: A pure chemical substance consisting of atoms of two or more different elements in fixed proportions (e.g., $NaCl$). Atoms are rearranged into new compounds via chemical bonds during chemical reactions.

• Natural State of Elements: Only a minority (e.g., Silver, Gold) are found as pure native minerals. Most occur as compounds or mixtures. Air is a mixture of nitrogen, oxygen, and argon, though it contains compounds like carbon dioxide ($CO_2$) and water ($H_2O$).

Periodic Table Trends and Valence

• Group Properties: Elements in the same vertical columns (groups) share similar chemical properties.

• Valence Electrons: The chemical behavior of an atom is determined by the number and arrangement of its outermost electrons.

• Energy Levels: Shells fill from the lowest energy level (closest to the nucleus) first.

• The Octet Rule: For an atom to be stable, its outer shell must be full.

Environmental and Earth Composition

• Abundance in Universe: Hydrogen is the most abundant element in the known universe.

• Abundance in Earth's Crust (Top $40\,km$ depth, which is $1\%$ of Earth's volume):

  • Oxygen is the most common element in the crust.

  • Aluminium is the most abundant metal in the crust.

  • Hydrogen is only the $10^{\text{th}}$ most abundant in the crust.

• Earth Layers:

  • Crust: Sea level to approx $40\,km$.

  • Mantle: Ranges from $100\,km$ to $2900\,km$ (boundary points mentioned at $670\,km$).

  • Outer Core: Extends from $2900\,km$ to $5150\,km$.

  • Inner Core: Extends from $5150\,km$ to $6371\,km$.

Human Body Composition

• Primary Elements: Over $99\%$ of atoms in the human body are comprised of four elements: Oxygen ($O$), Carbon ($C$), Hydrogen ($H$), and Nitrogen ($N$).

• Organic Compounds: Majority of biomolecules are compounds of carbon, termed organic compounds.

Principal Elements and Significance