Biochemistry

Molecular Bonding

  • importance:: bonds determine shape, shape has a big role in biology, structure and function are related
  • polar covalent:: valence electrons are unequally shared
    • ex - H₂O unequally shares electrons, so O is more electronegative
  • nonpolar covalent:: valence electrons shared equally
    • ex - O₂ electrons are equally shared
  • ionic:: transfer of electrons, forms an anion and cation
    • ex - NaCl
  • hydrogen bond:: weak bond between hydrogen and N, O, or F; results from polarity and electronegativity, occurs between molecules
    • ex - H₂O is polar, O has more electronegativity

Properties of Water

  • water polarity:: O is partially negative, H is partially positive, allows for other traits of water, allows hydrogen bonds
  • adhesion:: water sticks to something else (but not nonpolar substances), allows transpiration in plants
    • H₂O can move up a tube against gravity (ex - blood & capillaries)
  • cohesion:: water sticks to itself, high surface tension, also helps transport water in plants
  • high specific heat:: water absorbs a lot of energy before its temperature changes, prevents sudden rise in temp in living organisms

Acids and Bases

  • acids:: dissociate in water, release hydrogen ions
  • bases:: either take up hydrogen ions (H+) or release hydroxide ions (OH-), proton acceptor
  • pH scale:: 7 - neutral, less than 7 - acidic, more than 7 - basic
    • unit change in pH = 10x change in H+ concentration
  • buffers:: resist sharp changes in pH in aqueous solutions, acids and bases neutralize each other

Carbon

  • molecular diversity:: can form 4 chemical bonds to other atoms, small size fits into many large molecules
  • characteristics:: 4 valence electrons, forms 4 bonds, electroneutral, very stable, very available in environment
  • organization structures (isomers)
    • structural:: same formula, different order
    • cis trans:: same formula, different positioning around double bond
    • enantiomers:: same formula, mirror image positioning

Molecules

  • monomer:: molecule that can be bonded to other identical molecules to form a polymer
  • polymer:: substance made of smaller, simpler monomers
  • polymerization reactions
    • hydrolysis:: adding water to break bonds of polymers, results in monomers
    • dehydration synthesis:: remove water to join monomers to form new molecules

Lipids

  • structure:: contains CHO and sometimes P, hydrophobic fatty acid tails and hydrophilic phosphate group, nonpolar covalent bonds
  • monomer:: fatty acid chains and glycerol
  • polymer:: triglycerides
  • saturated fatty acid:: lack double bonds, straight hydrocarbon chains, help hormone production and protein signaling, solid at room temp
  • unsaturated fatty acid:: hydrocarbon chain, at least one double bond covalent bond, ends in carboxyl group
  • hydrophobic:: caused by nonpolar covalent bonds and hydrophobic fatty acid tails, mostly nonpolar C-H bonds

Carbohydrates

  • structure:: CHO in 1:2:1 ratio, normally in pentose or hexose rings, or chains
  • monomer:: monosaccharides (ex - glucose)
  • polymer:: polysaccharides (ex - cellulose, glycogen)
  • function:: main source of fast energy, forms ATP
  • positioning/order of molecules determines secondary structure
    • ex - starch and cellulose have same monosaccharides (glucose) but arranged differently

Proteins

  • primary structure:: linear amino acids (monomer), least denaturation when temp changes
  • secondary structure:: alpha helix or b-pleated sheet
  • tertiary structure:: most functional, random coil, S-S bonds, interacting R groups
  • quaternary structure:: coil of tertiaries, most affected by denaturation
  • polymer:: peptides
  • function:: structure, support, protection, catalysts, regulation

Enzymes

  • endergonic reaction:: energy absorbed, reaction isn’t spontaneous, requires energy to be driven
  • exergonic reaction:: energy released, reaction is spontaneous
  • anabolic pathway:: build complex molecules from simpler ones, need an input of energy
  • catabolic pathway:: break molecules into smaller units, release energy
  • function:: catalyze and speed up metabolic reactions, lower activation energy for a reaction, break down/build up substrate into product
  • catalyst:: increases rate of a chemical reactions without changing itself
  • active site:: part of enzyme that binds to the structure to form the product and help with the reaction
  • induced fit:: enzyme causes change in shape of substrate, contrasts lock and key fit
  • competitive inhibition:: substance with similar shape to substrate binds to and blocks active site
  • noncompetitive inhibition:: molecules bind to another part of the enzyme, changing its shape and function
  • feedback inhibition:: enzyme is inhibited by the substrate’s end product after interacting with the enzyme