General Biology/Getting Started/Matter

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The Nature of MoleculesEdit

MatterEdit

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 atomEdit

  • 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 isotopesEdit

  • 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

ElectronsEdit

  • 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 bondsEdit

  • 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 reactionsEdit

  • 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

WaterEdit

  • 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 bondingEdit

  • 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.

Last modified on 19 April 2010, at 19:34