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Biomolecules: Amino Acids and Proteins
 
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Last revised: Thursday, September 16, 1999
Reading: Ch. 5 in text
Note: These notes are provided as a guide to topics the instructor hopes to cover during lecture. Actual coverage will always differ somewhat from what is printed here. These notes are not a substitute for the actual lecture!
Copyright 1999. Thomas M. Terry

General Properties

  1. Most abundant biomolecule; accounts for 50% of dry weight.
  2. Built by assembling long chains of amino acids (monomers), followed by intricate folding
  3. Final shape of protein is very specific. Unless correctly folded, is not functional.
  4. several 1000 different types of proteins in any cell; millions of protein molecules
  5. To understand cellular life, must understand what different proteins are doing,how they work. A vast, but doable, challenge.
  6. Use study materials at The Biology Place to review the structure and function of proteins.

Variety of Functions

  1. rigid structure ; collagen in connective tissue, bone; keratin in fingernails and hair
  2. enzymes ; 3-D stereospecific chemical catalysts accelerate desired reactions by as much as 10 10 times over their spontaneous rates
  3. transport : membrane transport proteins carry substances across cell membranes; blood transport proteins that move certain substances (e.g., iron, oxygen, cholesterol) throughout the body.
  4. hormones ; chemical signals. Some hormones consist of as little as a single amino acid. Others are peptides or polypeptides. Example: insulin
  5. contraction ; muscle fibers, cilia, spindle fibers in mitosis.
  6. specific binding : e.g., antibodies that bind specifically to foreign substances to identify them to the body's immune system
  7. View Protein variety

Structure of Amino Acids

  1. Each amino acid has an amino group and a carboxyl group , joined by a single Carbon atom. In addition, each amino acid has a characteristic "side chain" (often called the -R group).
  2. View typical structure of an amino acid :
  3. Each amino acid (except glycine) can occur in two isomeric forms, L- and D-, because of the possibility of forming two different enantiomers (stereoisomers) around the central Carbon atom. Only L-amino acids are found in proteins in all organisms.
  4. View L- and D-valine
  5. Note: some D-amino acids are found in bacterial cell walls.
  6. Optional: Learn how to distinguish L- and D- amino acids by the CORN test .
  7. "R" side group can be any of 20 different chemicals.
  8. The most common amino acid, glycine, is only mildly nonpolar.
  9. Look at Fig. 5.15 in text to see other examples.
  10. The great variety of side chains allows proteins to have many different (chemical) properties, and to create many different environments.

Peptides and Polypeptides

  1. Amino acids are not accumulated by cells, but quickly joined into specific assemblies by the formation of peptide bonds .
  2. The peptide bond that binds amino acids is one of the strongest and most durable of covalent bonds. In the laboratory, we can break, or hydrolyze, peptide bonds most effectively by a combination of heat and acid. In your body, this digestive process begins in the stomach, where a combination of acid and enzymes help to break peptide bonds.If you didn't need to digest proteins, you wouldn't need a stomach!
  3. View formation of a peptide bond
  4. Two amino acids joined = dipeptide . Three AAs joined = tripeptide . Many AAs joined = polypeptide .
  5. Students often confuse the term polypeptide with the term protein. " Polypeptide " refers to the structure of a single chain. Every polypeptide has one free amino group (called the "N-terminus") and one free carboxyl group(called the "C-terminus"). " Protein " refers to the overall functional assembly, created when one or more polypeptides fold up and become functional units. Some proteins consist of only a single folded polypeptide chain, but many proteins contain multiple polypeptides, and frequently inorganic atoms as well, such as Zinc,Iron, Magnesium, etc.

Levels of Structure

1 o Structure

2 o Structure

  1. Polypeptides fold in a series of stages. The first level of folding is called the secondary (2 o ) structure.
  2. One of the most common 2 o folding patterns is called the alpha-helix , discovered by Pauling and Corey.
    • Alpha helix: Hydrogen bonds can form readily between C=O groups in the backbone and N-H groups four amino acid residues further along the chain.
    • This regular pairing pulls the polypeptide into a helical shape that resembles a coiled ribbon.
    • View alpha helix
  3. Another common folding pattern is called beta pleated sheet .
  4. Some protein regions remain in random coil, no regular pattern of secondary structure.
  5. Different proteins have different degrees of alpha helix, beta sheet, and random coil . Silk is a protein stabilized entirely by pleated sheet; keratin (in hair) is stabilized entirely by alpha helix. Most proteins have some of both.
  6. Review 2 o structure at The Biology Place.

3 o Structure

4 o Structure

If Chime plug-in is installed, View Tutorial on Insulin Structure for review.

Denaturation & Renaturation

  1. When proteins are heated, or exposed to acids or bases, or high salt concentrations, the variety of weak bonds holding tertiary and quaternary structure together can be disrupted so that the protein unfolds. Unfolding = denaturation resulting in loss of function.
  2. Unfolding can proceed even to disrupt secondary structure.
  3. Denaturation is sometimes reversible ; an unfolded protein can be restored to correct folding and regain biological activity. This is called renaturation .
  4. Denaturation can also occur irreversibly (as when egg white protein, albumin,is denatured by boiling to congeal as egg white). Renaturation is then no longer possible.

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