3.1 Amino Acids and Their Polymerization

• Most of these molecules are composed of just 20 different building blocks, called amino acids.

• In all 20 amino acids, a central carbon atom (referred to as the carbon) bonds covalently to four different atoms or groups of atoms:

  • H-a hydrogen atom

  • NH2-an amino functional group

  • COOH-a carboxyl functional group

  • a distinctive R-group”

• The combination of amino and carboxyl functional groups is key to how these molecules behave.

• The R-group, or side chain, represents the part of the amino acid core structure that makes each of the 20 different amino acids unique.

• Both polar and electrically charged R-groups interact readily with water and are hydrophilic.

• Nonpolar R-groups lack charged or highly electronegative atoms capable of forming hydrogen bonds with water. These R-groups are hydrophobic, meaning that they do not interact with water. Instead of dissolving, hydrophobic R-groups tend to coalesce in aqueous solution.

• If the R-group in your amino acid does not have a negative charge, a positive charge, or an oxygen atom, then you are looking at a nonpolar amino acid, such as methionine.

• The C-N covalent bond that results from this condensation reaction is called a peptide bond.

• There are three key points to note about the peptide-bonded backbone:

  • R-group orientαfion: The side chains of each residue extend out from the backbone, making it possible for them to interact with each other and with water.

  • Directionαnal: There is an amino group (-NH3 +) on one end of the backbone and a carboxyl group (-Coo-) on the other.

  • Flexibility: Although the peptide bond itself cannot rotate because of its double-bond nature, the single bonds on either side of the peptide bond can rotate. As a result, the structure as a whole is flexible

• Generally, when fewer than 50 amino acids are linked together in this way, the resulting polymer is called an oligopeptide (“few-peptides”) or simply a peptide.

• Polymers that contain 50 or more amino acids are called polypeptides (“many-peptides”).

• The term protein is often used to describe any chain of amino acid residues.

3.2 What Do Proteins Look Like?

• Biochemists refer to the unique sequence of amino acids in a protein as its primary structure.

• The next level of organization in proteins-secondary structure-is generated in part by interactions between functional groups in the peptide bonded backbone.

• In most proteins, these polar groups are aligned and form hydrogen bonds with one another when the backbone bends to form one of two possible structures:

  • an a-helix (alpha-helix), in which the polypeptide’s backbone is coiled

  • a B-pleated sheet (beta-pleated sheet), in which segments of a peptide chain bend 180° and then fold in the same plane

• A protein’s distinctive overall three-dimensional shape, or tertiary structure, results from interactions between residues that are brought together as the backbone bends and folds in space.

• There are five types of interactions involving R-groups that are important:

  • Hydrogen bonding

  • Hydrophobic interactions

  • Van de Waals interactions

  • Covalent bonding

  • Ionic bonding

• These disulfide (“two-sulfur”) bonds are frequently referred to as bridges, because they create strong links between distinct regions of 1e same polypeptide or two separate polypeptides.

• The combination of polypeptides, referred to as subunits, gives some proteins quaternary structure.

• In addition, cells contain macromolecular machines: complexes of multiple proteins that assemble to carηr out a particular function.

3.3 Folding and Function

• More recent work has shown that cells contain special proteins called molecular chaperones that can facilitate protein folding.

• Certain normal proteins can be induced to fold into infectious, disease-causing agents which are called prions.

3.4 Protein Functions Are as Diverse as Protein Structures

• Proteins are crucial to most tasks required for cells and organisms to exist:

  • Cαtαlysis Many proteins are specialized to catalyze, or speed up, chemical reactions. A protein that functions as a catalyst is called an enzyme.

  • Structure

  • Movement

  • Signaling

  • Transport

  • Defense

• Catalyzed reactions involve one or more reactants, called substrates.

• As researchers began to test Fischer's model, the location where substrates bind and react became known as the enzyme’s active site.