Atoms and Atomic Structure

Atoms

• Organisms are chemical machines
• Chemistry is important for understanding biology
• Matter comprises any substance in the universe with mass and volume
• All matter consists of atoms

Atomic Structure

• All atoms possess the same basic structure
• At the core of an atom is a dense nucleus containing 2 subatomic particles
• Protons: positively charged particles
• Neutrons: particles with no charge
• Orbiting the nucleus is a cloud of another type of subatomic particle
• Electrons: negatively charged particles

Characterizing Atoms

• Atoms are characterized by the number of protons or their overall mass
• Atomic number: the number of protons in the nucleus
• Mass number: the number of protons plus neutrons in the nucleus
• Electrons have negligible mass
• Atoms sharing the same atomic number exhibit the same chemical properties and belong to the same element

Electrons and Chemical Behavior

• Electrons dictate the chemical behavior of atoms
• Electrons position close enough to each other to facilitate interaction
• Electrons are associated with energy
• Electrons possess positional energy, called potential energy
• The field of energy around the electron is arranged as energy levels known as shells
• Orbitals within this volume are where electrons are most likely to be found

Electron Shells and Reactivity

• Electron shells have specific numbers of orbitals that fill with electrons
• Atoms featuring incomplete electron orbitals are more reactive
• Atoms gain, lose, or share electrons to completely fill their outermost shell
• Chemical bonding is based on these actions

Energy and Electron Levels

• Energy is released as electrons move closer to the nucleus to lower energy levels
• Moving electrons farther from the nucleus to higher energy levels requires energy

Ions

• Ions are atoms that gain or lose electrons
• A sodium atom loses one electron and becomes an ion positively charged
• A chlorine atom gains one electron and becomes an ion negatively charged

Isotopes

• Isotopes are atoms sharing the same number of protons but variable numbers of neutrons
• Most elements exist in nature as mixtures of different isotopes
• Isotopes of an element are usually chemically indistinguishable

Radioactive Isotopes

• Some isotopes are unstable and decompose into particles with lower atomic numbers, known as radioactive decay
• Radioactive isotopes have multiple uses
• Nuclear medicine
• Fossil dating

Radioactive Isotopes in Medicine

• Short-lived isotopes decay rapidly and do not harm the body
• Radioactive isotopes are used as tracers to study how the body functions

Fossil Dating

• The rate of decay of a radioactive element is constant
• Scientists can date fossils by measuring the fraction of radioactive elements that have decayed
• The older the fossil, the greater the fraction of radioactive atoms that have decayed

Molecules

• A molecule is a group of atoms held together by energy
• The energy is called a chemical bond
• Types of chemical bonds, from strongest to weakest:
• Covalent
• Ionic
• Hydrogen

Ionic Bonds

• Ionic bonds involve the attraction of opposite electrical charges
• Molecules comprised of these bonds are most stable as crystals

Covalent Bonds

• Covalent bonds form when atoms share electrons
• The number of electrons shared varies with the number needed to fill an atoms shell
• Covalent bonds are stronger than ionic bonds

Hydrogen Bonds

• Hydrogen bonds are weak bonds
• They form due to covalent bonds where one nucleus attracts electrons more than another
• Attraction for electrons by a nucleus is electronegativity
• Hydrogen bonds result in partial charges in atoms that unequally share electrons

Water and Covalent Bonds

• Water molecules contain two covalent bonds

Hydrogen Bonds and Polar Molecules

• Hydrogen bonds form in association with polar molecules
• Each atom featuring a partial charge acts like a magnet, bonding weakly with an oppositely charged polar atom
• The combined effects of hydrogen bonds can add collective strength to the bonds

Water and Life

• Water is essential for life, so biology relies on water chemistry
• Water is a polar molecule
• Water can form hydrogen bonds
• Hydrogen bonds give water special properties

Water Properties

• Water stores heat, and its temperature changes slowly
• Few hydrogen bonds break at low temperatures
  • Water becomes less dense when it freezes because hydrogen bonds stabilize, holding molecules farther apart
• Hydrogen bonds break at high temperatures
  • Water requires tremendous energy to vaporize because hydrogen bonds must be broken

Water Interactions

• Water molecules are sticky so they exhibit
• Cohesion via water molecules being attracted to one another
• Adhesion via polar molecules that are not water sticking to water
• Water is highly polar
• Water molecules in solution tend to form the maximum number of hydrogen bonds
• Hydrophilic molecules attract water and dissolve easily
• These molecules are polar and form hydrogen bonds
• Hydrophobic molecules are repelled by and do not dissolve in water
• These molecules are non-polar and do not form hydrogen bonds

Water Ionization

• The covalent bond within a water molecule breaks spontaneously
• This produces two ions in a process called ionization
• Due to the strength of covalent bonds, ionization does not occur often

pH

• pH measures the amount of ionized hydrogen from water in a solution
• The pH scale is logarithmic
• A pH scale difference of 1 unit represents a 10-fold change in hydrogen ion concentration
• Pure water has a pH of 7 and equal amounts of [H+] relative to [OH-]
• Substance that dissociates in water increases [H+] are called Acids
• Acidic solutions have pH values below 7
• Substances that combines with [H+] when dissolved in water are Bases
• Basic solutions have pH values above 7

pH and Organisms

• The pH in most living cells and their environments is close to 7
• Proteins involved in metabolism are sensitive to pH changes
• Acids and bases are regularly encountered by living organisms
  • From metabolic activity such as chemical reactions
  • From dietary intake and processing
• Organisms use buffers to minimize pH disturbances

Buffers

• A buffer is a chemical substance that takes up or releases hydrogen ions
• Buffers do not remove the acid or base affecting pH but minimize their effect on it
• Most buffers are pairs of substances, one an acid and one a base