General Biology/Getting Started/Matter

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Matter

Matter is defined as anything that has mass (an amount of matter in an object) and occupies space (which is measured as volume).

• Particles, from smallest to largest
  1. Subatomic particles
     • Electrons
     • Protons
     • Neutrons
  2. Atoms
  3. Molecules
  4. Macromolecules
• Origin of matter
  1. Big Bang, about 13.7 billion years ago
  2. Hydrogen, helium
  3. Heavier elements formed in suns, super nova
     • Earth's matter predates formation of sun, 4.5 billion years ago
• All matter consists of atoms, which are composed of : electrons, protons, neutrons

The atom

• Example: Hydrogen
  • The simplest element
  • One proton (+)
  • One electron in orbit (-)
• Built by adding one proton (and one electron) at a time
• Number of protons determines atomic number and number of electrons
• Neutrons
  • Neutral charge
  • Contribute mass
  • May decay
• Oxygen
  • 8 protons (mass)
  • 8 electrons
  • 8 neutrons (mass)

Mass and isotopes

• Atomic mass
  • Sum of masses of protons and neutrons
  • Measured in daltons or AMU (Atomic Mass Unit)
  • An AMU is 1/12 the mass of Carbon-12
  • proton ~1 AMU or dalton
  • 6.024 x 10²³ daltons/gram
• Atoms with same atomic number belong to same element
• Isotopes
  • Same atomic number but different atomic mass
  • Some are radioactive
  • Uses of isotopes
    • Radioactive: 3H, 14C, 32P, 35S
      • Tracers in biochemical reactions
      • Detection of molecules in recombinant DNA technology (genetic engineering)
      • Half-life: dating of rocks, fossils
    • Non-radioactive (N, C, O)
      • Diet of organisms (including fossils)
      • Biochemical tracers

Electrons

• Negative charge
• Held in orbit about nucleus by attraction to positively charged nucleus
• Atom may gain or lose electron, altering charge
  • Cation: loses electron, positive charge
    • Na⁺
  • Anion: gains electron, negative charge
    • Cl^-
• Determine chemical properties of atoms
  • Number
  • Energy level

Chemical bonds

• Form molecules
• Enzymes: make, break, rearrange chemical bonds in living systems
• Ionic
• Covalent
  • Sharing of one or more pairs of electrons
    • Called single, double, or triple
  • No net charge (as in ionic bonds)
  • No free electrons
  • Give rise to discrete molecules
  • Hydrogen

Chemical reactions

• Formation and breaking of chemical bonds
• Shifting arrangement of atoms
• Reactants -> products
• Reactions are influenced by:
  • Temperature
  • Concentration of reactants, products
  • Presence of catalysts (enzymes)
• Oxidation:reduction

Water

• Essential for life
• ~75% earth's surface is water
• Life evolved in water
• Solvent for many types of solutes
• High specific heat
• High polarity
  • Creates a slightly negative Oxygen and a Slightly positive hydrogen
  • allows formation of Hydrogen Bonds

Hydrogen bonding

• A type of polar interaction
• Critical for:
  • Protein structure
  • Enzymatic reactions
  • Movement of water in plant stems
• Weak and transient
• Powerful cumulative effect
  • Solubility of many compounds
  • Cohesion (capillary action)
  • Lower density of ice
• Formed between molecules other than water
  • Protein structure
  • DNA, RNA structure

Water organizes nonpolar molecules

• Nonpolar molecules: no polarity (+/-) charges
• Hydrophobic: exclude water because they don't form hydrogen bonds with it
• Consequences:
  • Membranes
  • Protein structure
• Hydrophilic: polar substances associate with water

Ionization of water: H₂O -> H⁺ + OH^-

• Forms a Hydrogen ion (H⁺), hydroxide ion (OH^-)
• Due to spontaneous breakage of covalent bond
• At 25°C, 1 liter of water contains 10-7 moles of H⁺ ions: 10-7 moles/liter

pH

• A convenient way of indicating H⁺ concentration
• pH = -log[H⁺]
• For water, pH = -log[10-7] = 7
• Since for each H⁺ in pure water, there is one OH^-, pH of 7 indicates neutrality
• Logarithmic scale

Buffer

• Reservoir for H⁺
• Maintains relatively constant pH over buffering range

Reference

This text is based on notes very generously donated by Dr. Paul Doerder, Ph.D., of the Cleveland State University.