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.