From Biolk483


Dissolving stuff in Water

  • returning to the hexane exmaple:
    • hexane cannot form h-bonds with water because c-h bond isn't electronegative
    • so only two h-bonds can be made when the oxygen is facing the hydrocarbon (the two bonds are its hydrogens h-bonding with two other water molecules' oxygen atoms), therefore the water molecules want to be down in the cloud of water molecules and we experience surface tension
    • anytime you put a hydro-carbon in water you make a new surface; any new surface takes more energy.
  • Entropy can help explain the hydrophobic effect
    • we'll consider entropy as a number representing randomness (the higher the number the greater the randomness)
    • in nature, entropy is maximized
    • in this example, the entropy of hexane decreases as it forms into a ball trying to get away from the water, so that seems strange as we just said that nature maximizes entropy
    • however, as the hexane forms into a ball, the entropy of water (which there is significantly more of) increases therefore increasing the entropy of the entire system. Then, this makes sense that entropy is maximized by this process.

Hydrophillic effect

  • something that likes water (probably because it is polar or charged)
  • most large biologic molecules have both phillic and phobic areas.
  • this dichotomy is responsible for all biochemical shapes
  • true in membranes, proteins and nucleic acids


What is a protein

  • linear arrangement of amino acids
  • no branching off the amino acid chain
  • held together by peptide bonds
  • how big?: no upper or lower bound really
    • smallest protein is around 5k atomic mass units (so an aa chain must be greater than this to be considered a protein, although this number is arbitrary)
      • we call things with 1 aa an amino acid
      • we call things with 2 aa a dipeptide (they are hooked by peptide bond)
      • we call things with 3 aa a tripeptide
      • etc.
      • several aa = oligopeptide (too many to name, but not too many)
      • less than 100 aa = polypeptide
      • more than 100 aa = protein
    • generally between 50k and 100k amu
    • lower limit is based on insulin (which is 5300 amu)
      • Why insulin you ask? (because it is important and has biochemical history)
  1. Banting and Best isolated insulin out of pancreas in 1922 to treat diabetes. They got a Nobel Prize.
  2. 1955, Sanger sequenced insulin. He got a NP (and a second NP for sequencing nucleic acids.)
  3. Humulin; sold by Eli Lilly is one of the first genetically engineered products (and one of the best selling, still)

Hydrolysing a protein

  • this means to break it up using water
  • when simple proteins are broken down they just give off amino acids
  • when nucleoproteins are broken down they give off amino acids and nucleic acids
  • when lipoproteins are broken down they give off amino acids and lipids
  • when glycoproteins are broken down they give off amino acids and sugars
  • when metaloproteins are broken down they give off amino acids and metals
  • when flavoproteins are broken down they give off amino acids and FAD(?)

Functions of Proteins

  • this is the most important function
  • proteins that catalyze are called enzymes
  • there are about 2k different reactions to be catalyzed in our body
  • not all enzymes are proteins: small RNAs can put two nucleotides together
  • these proteins have no dynamic movement really
  • these are just collections of amino acids to be used to make other aa
  • example: ovalbumin, caselin
Transport within Organism
  • examples:
    • serum albumin: picks up stuff in blood
    • hemoglobin carries oxygen
    • calmodulin carries Calcium
Transmembrane Transport
  • A primary example that we will give attention to this semester: the sodium potassium ATPase:
    • sodium gets pumped out while potassium is pumped in which creates an electrical gradiant
    • then the motor makes ATP
    • uses 1/3 of energy we consume each day to make this gradiant
Contractile Proteins
  • myosin and actin
  • muscle contraction, moving things around the cell
  • antibodies like Fibirojen(?)
  • venom, defense mechanisms, etc.
  • yeah...hormones.
Physical Support
  • aka structure
  • collagen (humans have more collagen than any other protein)
  • sit on surface of cell and bind to stuff, etc.
  • transcription factors, etc.

Amino acids

  • building blocks of proteins
  • has an amine group
  • so we have alpha and beta but beta amino acids are relatively unimportant
  • the alpha carbon is assymetric (except in glycine where the R-group is a hydrogen)
    • so amino acids are optically active
    • we have nearly only L proteins because use L amino acids to build them.
    • we have d-aminooxidase to get rid of D amino acids because they can cause trouble
  • we don't know why L > D, but we think it occured via the catastrophe theory somewhere along the path of evolution.
    • if we get a sample from outer space and it is racemic then there is only chemical evolution occuring there, but if it is primarily L or primarily D then it is the result of biological evolution.
  • be sure to know the structural difference between the L and D amino acids
  • There are 20 R-groups that define the 20 amino acids that are coded for in our DNA
    • There are 100s and 100s of amino acids, but these 20 are found in our genetic code, however.
    • Know the structure and 3-letter code for each of the twenty.
    • There are three important things to note:
  1. glycine is not optically active
  2. isolucine has two chiral carbons giving it two optically active carbons
  3. threonin also has a second carbon that is optically active
Charge and Amino Acids
  • There are some r-groups that can lose electrons pretty easily making them charged amino acids.
  • Much material on pKa here and in the next lecture....
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