BIOCHEM L1

• Four main groups of biomolecules:

  • Proteins (peptides or polymers of amino acids)
  • Lipids (nutrition)
  • structural, energy storage, hormones
  • Carbohydrates (Monosaccharides and polysaccharides)
  • energy storage and cell signaling, structural functions
  • Nucleic Acids (DNA, RNA, nucleotides)
  • storage of genetic information, structural, energy storage, energy metabolism
• biochemistry is principally concerned with the chemistry and molecular interaction of biological interactions of biological molecules associated with living systems
• bios = life (greek)
• al kimya = the transmutation (Arabic)
• Chemistry explains "change" using atoms
• all chemical change involves rearrangements of electrons
• biochemistry explains life in terms of atomic structures of biological molecules and the chemical changes they undergo when they interact with other biological and non-biological molecules
• biosphere contains more than 10^6 different species ranging from single cells to complex animals
• all life forms use the same type of biomolecules and all share some common metabolic features suggesting a common ancient ancestor with variation on a theme over time
• change = chemical reactions
• most biochemical reactions are mediated by enzymes
• enzymes are proteins that catalyze biochemical reactions
• enzymes have catalytic activity as a function of their molecular structure
• proteins are composed of amino acids
• to understand the properties of amino acids (and most other biochemical molecules) we must review water, buffers and pH
• synthesis and degradation of biomolecules and other transformations associated with life:

  • metabolism
  • catabolism
  • anabolism
• Metabolism: organized network of reactions occurring in cells
• Catabolism: reactions that degrade (breakdown) nutrient molecules yielding energy
• Anabolism: Cell components are assembled (making) from small molecules and energy
• Bond strength depends on the properties of the atoms including

  • electronegativity
  • functional groups
  • saturated hydrocarbons
  • H- bonds
  • enthalpy
  • electrostatic interactions
  • van der waals interaction
  • amphipathic molecules
• Electronegativity: a measure of the ability of an atom in a molecule to attract electrons to itself
• Hydrogen (H): 2.1
• Nitrogen (N): 3.0
• Phosphate (P): 2.1
• Carbon (C): 2.5
• Oxygen (O): 3.5
• Sulfur (S): 2.5
• Biomolecule reactivity is found in functional groups that have polar bonds
• C-O is a carboxyl or carbonyl
• H-O is an alcohol
• H-N is an amino
• H-S is a Thiol or Sulfhydryl
• P-O is a phosphate or phosphoryl
• there are 5 different types of biochemical transformations involving bond formation or bond breakage

  • group transfer (CH3, typically)
  • oxidation-reduction (changing electrons)
  • rearrangement (complex)
  • cleavage (1 to 2)
  • condensation (putting them together)
• Molecules with mostly C-H and C-C bonds are called saturated hydrocarbons and are non-polar or only slightly polar and tend to be non-reactive, have lots of energy under normal conditions
• C-O bond is polar
• water or H20 is of central importance to biochemistry because it is the main solvent of the cell
• Biochemistry looks at their chemical structures and molecular functions
• Chemistry is what is happening with electrons and between atoms
• polar parts will typically drive things