Proteins (College Board AP® Biology)

Molecular Structure of Proteins

Proteins

• Proteins are polymers (and macromolecules) made of monomers called amino acids

• The sequence, type and number of the amino acids within a protein determine its shape and, therefore, its function

• Proteins are extremely important in cells because they form all of the following:

  • Enzymes

  • Cell membrane proteins (eg, carrier)

  • Hormones

  • Immunoproteins (eg, immunoglobulins)

  • Transport proteins (eg, hemoglobin)

  • Structural proteins (eg, keratin, collagen)

  • Contractile proteins (eg, myosin)

• Because all genes that get expressed code for proteins, all of the reactions necessary for life are dependent on the function of proteins

Amino Acid Structure

• Amino acids are the monomers of polypeptides

• There are 20 amino acids found in polypeptides common to all living organisms

The general structure of all amino acids is a central carbon atom bonded to:

• An amino group -NH₂

• A carboxylic acid group -COOH

• A hydrogen atom

• An R group (which is how each amino acid differs and why amino acid properties differ eg, whether they are acidic or basic or whether they are polar or nonpolar)

• The R group can be as simple as another hydrogen atom (glycine), right through to complex aromatic ring structures (eg, phenylalanine)

Diagram of the Generalized Structure of an Amino Acid

The generalized structure of an amino acid

Peptide bonds

• To form a peptide bond a hydroxyl group (-OH) is lost from the carboxylic group (-COOH) of one amino acid and a hydrogen atom is lost from the amino group (-NH2) of a neighboring amino acid

• The remaining carbon atom (with the double-bonded oxygen) from the first amino acid bonds to the nitrogen atom of the second amino acid

• This is a dehydration synthesis reaction so water is released

• Dipeptides are formed by the dehydration synthesis of 2 amino acids

• Polypeptides are formed by the dehydration synthesis of many (3 or more) amino acids

• A protein may have only 1 polypeptide chain or it may have multiple chains interacting with each other

• During hydrolysis reactions, the addition of water breaks the peptide bonds, resulting in polypeptides being broken down into amino acids

Diagram of Formation and Hydrolysis of a Peptide Bond

Amino acids are bonded together by covalent peptide bonds to form a dipeptide in a dehydration synthesis reaction

Categories of Amino Acid by R Group

• The R Groups of the 20 amino acids fall into 3 categories

• These are based on the properties of the side chains (R groups) 

  • Hydrophobic (nonpolar side chains)

  • Hydrophilic (polar side chains)

  • Some hydrophilic amino acids are acidic or basic, based on the ionization of their side chain groups (-COOH or -NH₂) 

    • These side chains are distinct from the -COOH and -NH₂ groups that all amino acids possess attached to their central carbon atom

• The interactions between the different R groups in a polypeptide chain determine the 3-D shape of the protein

  • And, in turn, the properties of the protein