9/1/00  Lecture, Bio 130, Chapter 5- Proteins

Organizational notes:

If you haven’t done the BioCoach exercise Building Biomolecules, you should do it ASAP.  Go through BioCoach exercise  Properties of Biomolecules.  Be sure to do all the practice and review portions- they are the most valuable part. 

Study groups are a great way to study and prepare for exams.  We  advise you to start thinking about forming one.  The class email list is a good way to start.  Also, we are going to have a peer advisor, Jenn Pang at the CTL (she is the Thursday lab TA).  We will announce her schedule when it is finalized.

1.  Proteins:  The Molecular Tools of the Cell 

Please note that “protein” is spelled “protein”- a common error is “protien”

• Proteins account for > 50% of the dry weight of cells, and they are instrumental in almost everything organisms do.  (Table 5.1, modified below)

• Proteins are the most structurally sophisticated molecules known.  Vary extensively in structure, with each type of protein having a unique three-dimensional shape, or conformation. 
• All proteins are polymers of the same set of 20 amino acids.  Polymers of amino acids are called polypeptides.  A protein consists of one or more polypeptides folded and coiled into a specific conformation.

2. Amino acids

• Monomers for polypeptides
• Basic structure: at the center of the amino acid is an asymmetric carbon.  Its four different partners are an amino group, a carboxyl group, a hydrogen atom, and a variable group symbolized by R.  The R group, or side chain, differs with the amino acid.
• Classified into four groups on basis of R groups, see Figure 5.15
• Nonpolar
• Polar
• Electrically charged: acidic (- charge, carboxyl group)
• Electrically charged: basic (+ charge, amino group)
• Use Chime to view amino acid structures
• Top part of right hand screen in Antibody, Hemogloblin, or MHC; see also "Chime's Menu" at the bottom of this screen for instructions on useful Chime commands
• Website with comparison of amino acid structures
• Website where you can look at amino acids within a protein

 3.      Peptide bonds

• When two amino acids are positioned so that the carboxyl group of one is adjacent to the amino group of the other, an enzyme can join the two by means of a dehydration reaction.
• The resulting covalent bond is called a peptide bond.

 4.      Polypeptide not necessarily = a protein

• A protein is one or more polypeptides precisely twisted, folded, and coiled into a molecule of unique shape. 
• The amino acid sequence of the polypeptide determines what its three dimensional shape will be.

 5.      There are four levels of protein structure

• Primary
  • amino acid sequence
• Secondary
• Coils and folds in polypeptide chain. Result from hydrogen bonds that occur at regular intervals along the polypeptide backbone.   Hydrogen bonds occur between the H attached to the N of the polypeptide backbone and the O of the polypeptide backbone.  Individually these H bonds are weak, but collectively they support and maintain the particular shape.
• a helix
• b pleated sheet
• Examples can be seen in Chime structures of Hemoglobin (lots of a helix), Antibody (lots of b pleated sheet) and MHC molecules (both forms)
• Try the Protein Roller Coaster Movie
• Tertiary
• Total conformation of polypeptide
• Consists of irregular contortions from bonding between side chains of the various amino acids
• Quaternary
• All of polypeptides that form a protein

 6.      How does protein folding occur?

• As protein is synthesized
• Chaperone proteins

 7.      Denaturation

• Certain conditions will cause a protein to lose its configuration. 
• Includes pH, salt concentration, temperature, etc.