Chapter 3- Protein Structure and Function

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.