Proteins

• Amino acids are the monomers of protein molecules
• Monomers are subunits, or “building blocks”
• Polymers are what you get when you string many monomers together
• Each amino is composed of a central carbon atom attached to:

  1. Amino group (NH2)
  2. Carboxyl group (COOH)
  3. Hydrogen (H)
  4. R groups
• There are 20 different amino acids, defined bytheir unique R group
• The 20 amino acids can be grouped based on:• How they interact with water (hydrophilic vs. hydrophobic)• Whether they are basic or acidic
• Properties of amino acids are very importantbecause they influence how a proteinfolds into its 3D shape
• Protein shape determines protein functions
• By stringing different amino acid monomers together in all kinds of unique ways and combinations to create unique protein polymer
• The carboxyl group of one amino acid can react with the amino group of another to form a covalent bond called a peptide bond
• When many amino acids are linked, the resulting polymer molecule is a polypeptide
• Polypeptide is basically an immature protein
• The unique sequence of amino acids that make up a polypeptide strand is called the primary structure of a protein
• A protein’s primary structure determines its shape and thus its function
• In other words, the primary structure determines:

  • How the protein “folds” into its 3D shape, then....
  • The 3D shape determines which parts of the protein can interact with other molecules or ions in the cell (...thus, determines its function)
• A change of even one amino acid in the primary structure canmake an entirely different protein
• The primary polypeptide strand is progressively folded into its final 3D shape in 2-3 “steps,” or “structural levels”
• A protein’s primary structure is its unique sequence of amino acids that form the linear polypeptide strand
• Folding the primary structure gives us an intermediate shapecalled the secondary structure
• A protein’s secondary structure is stabilized (supported) byH-bonding along the polypeptide backbone
• B/c the peptide backbone is flexible and lined with δ+ and δ- charges, it can twist and bend around itself to allow parts of the peptide backbone to form hydrogen bonds with each other
• There are 2 common types of secondary structures aprimary polypeptide will fold into

  1. ALpha Helices
  2. Beta Sheets
• Alpha Helix

  • The carbonyl (C=O) group of each amino acid in the backbone forms a hydrogen bond with the amide group (N-H) of the amino acid 4 residues away
• Beta Sheet

  • Instead of twisting into a helix, polypeptide bends over,creating parallel, adjacent strands. Hydrogen bonds formbetween carbonyl groups along one length of the strandand the amide groups along the adjacent strand (it’s stillall one polypeptide)
• Secondary structure results from hydrogen bonding along the backbone (between the carboxyl group of one amino acid and the amide group of another) to form alpha helices and/or beta sheets
• A polypeptide’s tertiary structure is its final folded 3D shape
• The tertiary structure of a polypeptide is made up of several secondary structure elements (often a combination of alpha helices and beta sheets)
• Whereas secondary structures are formed by hydrogen bonding along the polypeptide backbone...A polypeptide’s tertiary structure results from interactionsbetween side groups (R)
• tertiary structure is mostly determined by:

  • Interactions between R groups and the surrounding water
  • Interactions between different R groups within the polypeptide
• R groups have different chemical properties so:

  • They can be hydrophilic or hydrophobic
  • They can be polar or nonpolar
  • They can be basic or acidic
• The R-group interactions that determine the complex, 3D shape of a polypeptide’s tertiary structure can be both short- and long-range
• Hydrophobic interactions play a HUGE contributing role in the folding and shaping of a protein
• Hydrophilic R groups seek contact with their aqueous environment
• Hydrophobic R groups will seek to avoid water and thus position themselves towards center of protein (away from aqueous environment)
• Hydrogen bonding (and other intermolecular forces, such as van der Waal forces interactions) help to stabilize protein structure
• H-bonding in polypeptide chain and between amino acid R groups hold the protein in the shape established by hydrophobic interactions
• van der Waals forces are interactions between attractive and repulsive forces that occur between R groups that become polarized
• Due to protein folding, ionic bonding can occur between thepositively and negatively charged "R" groups that come in close contact with one another
• Folding can also result in covalent bonding between the "R" groups of cysteine amino acids, forming a disulfide bridge
• Protein folding usually happens spontaneously(to some extent)