General Properties

• Most abundant biomolecule; accounts for 50% of dry weight.
• Built by assembling long chains of amino acids (monomers), followed by intricate folding
• Final shape of protein is very specific. Unless correctly folded, is not functional.
• several 1000 different types of proteins in any cell; millions of protein molecules
• To understand cellular life, must understand what different proteins are doing,how they work. A vast, but doable, challenge.

Variety of Functions

• rigid structure ; collagen in connective tissue, bone; keratin in fingernails and hair; silk fibers
• enzymes ; 3-D stereospecific chemical catalysts accelerate desired reactions by as much as 10 ¹⁰ times over their spontaneous rates. View enzyme (green) interacting with substrate.
• transport : membrane transport proteins carry substances across cell membranes; blood transport proteins that move certain substances (e.g., iron, oxygen, cholesterol) throughout the body.
• hormones ; chemical signals. Some hormones consist of as little as a single amino acid. Others are peptides or polypeptides. Example: insulin
• contraction ; muscle fibers, cilia, spindle fibers in mitosis. View animation of actin-myosin interaction to produce muscle contraction
• specific binding : e.g., antibodies that bind specifically to foreign substances to identify them to the body's immune system
• View Protein variety
• Review protein functions (Activity 5E, from Campbell 6th Ed. website)

Structure of Amino Acids

• 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).
• View typical structure of an amino acid :
• 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.
• View L- and D-valine
• Note: some D-amino acids are found in bacterial cell walls.
• Optional: Learn how to distinguish L- and D- amino acids by the CORN test .
• "R" side group can be any of 20 different chemicals.
  1. View amino acids with nonpolar side chains
  2. View amino acids with polar side chains
  3. View amino acids with electrically charged side chains
• The most common amino acid, glycine, is only mildly nonpolar.
• Look at Fig. 5.15 in text to see other examples.
• 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

• Review protein structure (Campbell website activity)

1 ^o Structure

• 1 ^o structure = specification of the sequence of amino acids.
• View example: a tetrapeptide
• Note: since every polypeptide begins with free amino group, this is called the N-terminus. The opposite end of the polypeptide has a free carboxyl group, called the C-terminus.
• View primary structure (Campbell website activity)

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 .
   • View beta sheet
4. View secondary structure (Campbell website activity)
5. Some protein regions remain in random coil, no regular pattern of secondary structure.
6. 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.

3 ^o Structure

• Polypeptides continue folding beyond the formation of secondary structure. It is only with the complete, compact folding into tertiary (3 ^o ) structure that they attain their "native conformation" and become active proteins (as a result of the creation of active sites).
• View tertiary structure (Campbell website activity)
• Forces that contribute to tertiary folding include:
  1. hydrogen bonds
  2. hydrophobic bonds
  3. ionic bonds
  4. sulfhydryl bonds (-S-S- bonds). These are especially important, because they are covalent bonds and quite strong compared to H-bonds.

4 ^o Structure

• Some proteins are made of multiple polypeptide subunits, which must be assembled together after each individual polypeptide has reached its 3 ^o structure. Examples:
  1. Hemoglobin (blood protein involved in oxygen transport) has four subunits .
     View Hemoglobin molecule
  2. Pyruvate dehydrogenase (mitochondrial protein involved in energy metabolism) has 72 subunits .
• View quaternary structure (Campbell website activity)

Using Chime Plugin as a tool to help visualize structure

• What is Chime?
• Download the free Chime plugin. Note that CHIME does not work with all web browsers -- pay attention to notes at the download site regarding compatibitily.
• If Chime plug-in is installed, View Tutorial on Insulin Structure for an excellent self-guided tour.
• Chime: How to use it: a quick tutorial

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.