Proteins (College Board AP® Biology): Study Guide

Structure & function in proteins

• Proteins are made of linear chains of monomers called amino acids

• The amino acids are connected by covalent bonds (peptide bonds) at one end of the growing peptide chain

• 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, e.g. carriers

  • hormones

  • immunoproteins, e.g. immunoglobulins

  • transport proteins, e.g. hemoglobin

  • structural proteins, e.g. keratin and collagen

  • contractile proteins, e.g. myosin

• All genes that are expressed will code for specific proteins, therefore 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 specific order of amino acids in the overall protein polypeptide (referred to as its primary structure) determines the overall shape of the protein

• Within an amino acid, a central carbon atom is bonded to:

  • an amino terminus (NH₂)

  • a carboxylic acid terminus (COOH)

  • a hydrogen atom

  • an R group

    • The R group of an amino acid can be categorized by its chemical properties (hydrophobic, hydrophilic, or ionic)

    • The interactions of these R groups determine the structure and function of that region of the protein

Peptide bonds

• Amino acids are connected by the formation of peptide bonds at the carboxyl terminus of the growing peptide chain.

• To form a peptide bond:

  • a hydroxyl group (-OH) is lost from the carboxylic group (-COOH) of one amino acid

  • a hydrogen atom is lost from the amino group (-NH2) of the 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 two amino acids

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

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

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

Protein structure

• There are four levels of structure in proteins:

  • Three are related to a single polypeptide chain and the fourth level relates to a protein that has two or more polypeptide chains

• The four elements of protein structure determine the function of a protein

• Polypeptide or protein molecules can have anywhere from three amino acids (Glutathione) to more than 34,000 amino acids (Titan) bonded together in chains

Primary

• Proteins have a primary structure determined by the sequence order of their amino acids

• DNA within a cell determines the primary structure of a protein by instructing the cell to add certain amino acids in specific quantities in a certain sequence

  • This affects the shape and therefore the function of the protein

• The primary structure is specific for each protein (one alteration in the sequence of amino acids can affect the function of the protein)

Secondary

• The secondary structure arises from the folding of the amino acid chain into different shapes

• The secondary structure of a protein is held together by hydrogen bonds that form between the -NH region of one amino acid and the -C=O region of another

  • The hydrogen of -NH has an overall positive charge while the oxygen of -C=O has an overall negative charge

• Two shapes can form within proteins due to the hydrogen bonds:

  • α-helix

  • β-pleated sheet

• The α-helix shape occurs when the hydrogen bonds form between every fourth peptide bond

• The β-pleated sheet shape forms when the protein folds so that two parts of the polypeptide chain are parallel to each other, enabling hydrogen bonds to form between the folded layers

• Hydrogen bonds are relatively weak so can be broken easily by high temperatures and pH changes

Tertiary

• Tertiary structure is the overall three-dimensional shape of the protein

• Additional bonds are formed between the R groups of the amino acids

• The additional bonds can be:

  • hydrogen bonds between R groups

  • disulphide bonds between cysteine amino acids

  • ionic bonds between charged R groups

  • weak hydrophobic interactions between non-polar R groups

• The tertiary structure of proteins often minimizes free energy

  • This is because the folded structure with the lowest free energy is the most stable conformation

• Tertiary structure is common in globular proteins

Quaternary

• Quaternary structure arises from interactions between multiple polypeptide units where more than one polypeptide chain works together as a functional macromolecule, e.g. haemoglobin

• Each polypeptide chain in the quaternary structure is referred to as a subunit of the protein