Chapter 2 Basic Chemistry

Chapter 2: The Chemical Context of Life

Basic Chemistry: Matter, Elements, & Compounds

• Organisms are composed of matter.

• Matter: Anything that occupies space and has mass.

• Matter is formed from elements.

Elements and Compounds

• Element: A substance that cannot be broken down into simpler substances via chemical reactions.

• Compound: A substance formed from two or more elements combined in a fixed ratio.

  • Has emergent properties that differ from its individual elements.

Elements in the Human Body (Table 2.1)

• Major elements include:

  • Oxygen (O): 65.0%

  • Carbon (C): 18.5%

  • Hydrogen (H): 9.5%

  • Nitrogen (N): 3.3%

  • Calcium (Ca): 1.5%

  • Phosphorus (P): 1.0%

  • Trace elements (e.g., Iron, Iodine) exist in very small quantities (<0.01%).

Toxic Elements

• Some elements can be toxic.

• Some species have adapted to environments containing toxic elements.

Atoms

• Each element consists of unique atoms.

• Atom: The smallest unit of matter that retains properties of an element.

Subatomic Particles

• Atoms comprise three types of subatomic particles:

  • Electrons: Negatively charged particles located in electron shells.

  • Protons: Positively charged particles found in the nucleus.

  • Neutrons: Neutral particles found in the nucleus.

Atomic Structure

• Atoms vary by their number of subatomic particles.

• Electrons occupy a "cloud" around the nucleus.

Atomic Number and Atomic Mass

• Atomic Number: Number of protons in the nucleus;

  • Defines the element and equals the number of electrons in a neutral atom.

• Mass Number: Sum of protons and neutrons in the nucleus.

• Atomic Mass: Total mass of an atom approximated by mass number.

  • Protons and neutrons have a mass of roughly 1 Dalton (1.7 x 10^-24 grams).

  • Electrons are negligible in the mass calculation.

Isotopes

• Isotopes: Atoms of the same element differing in the number of neutrons.

• Atomic mass reflects the weighted average of isotopes.

• Radioactive Isotopes: Decay spontaneously, emitting particles and energy.

Radioactive Tracers and Dating

• Radioactive isotopes used in medicine as diagnostic tools.

• Radiometric Dating: Measures isotopes' ratio to estimate the time since formation of fossils/rocks using half-lives.

  • Example: Carbon-14 decays with a half-life of 5,700 years.

Energy Levels of Electrons

• Potential Energy: Stored energy due to an electron's position.

• Electrons exist in distinct energy levels or shells, with varying potential energy.

• Changes in these energy levels occur in fixed increments.

Electron Distribution and Chemical Properties

• Chemical behavior determined by the arrangement of electrons, particularly valence electrons.

• Valence Electrons: Outermost shell electrons that determine chemical interactions.

Chemical Bonding

• Covalent Bonds: Formed by the sharing of valence electrons. The forms are:

  • Single Bond: Sharing one pair of electrons.

  • Double Bond: Sharing two pairs of electrons.

• Ionic Bonds: Formed between oppositely charged ions (anions and cations) due to electron transfer.

• Hydrogen Bonds: Attraction between a hydrogen atom covalently bonded to electronegative atoms (especially O and N).

• Van der Waals Interactions: Weak attractions that can be significant collectively.

Molecular Shape and Function

• Shape influences function; based on the arrangement of atomic orbitals (hybridization).

• Example: Similar shapes of opiates and endorphins lead to similar biological effects.

Chemical Reactions

• Involve making and breaking of chemical bonds.

• Photosynthesis: A key reaction converting CO2 and water into glucose and oxygen.

• Reversible reactions reach equilibrium when reaction rates of forwards and backwards are equal, maintaining constant concentrations of reactants and products.