General Biology/Getting Started/Matter

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General Biology | Getting Started | Cells | Genetics | Classification | Evolution | Tissues & Systems | Additional Material


The Nature of Molecules[edit]

Matter[edit]

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
    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[edit]

  • 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[edit]

  • 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[edit]

  • 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[edit]

  • 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[edit]

  • 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[edit]

  • 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[edit]

  • 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

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