Amino acids are the basic units that make up proteins. Each amino acid has a similar structure: amino group (-NH₂), carboxyl group (-COOH), hydrogen atom and other atomic groups (-R) all attached to the same carbon atom. The type of amino acid is determined by its R group. The R group is arbitrary theoretically, but there are only 20 amino acids that make up proteins. Amino acids are classified according to the character of R group.
Hydrophobic amino acids: their R groups are hydrophobic (Gly, Ala, Val, Leu, Ile, Met, Phe, Trp, Pro)
Hydrophilic amino acids: their R groups are hydrophilic. They are classified again into neutral amino acids, basic amino acids, acidic amino acids.
Neutral amino acids: their R group contain a polar hydroxyl or carbonyl group and is not charged (Ser, Thr, Cys, Tyr, Pro)
Basic amino acids: their R group contain amino group, positively charged (Asp, Glu)
Acidic amino acids: their R group contains hydroxyl group, negatively charged (Lys, Arg, His)
The four levels of protein structure
Each protein has a unique three-dimensional structure that can be combined with specific molecules to perform the corresponding biochemical reactions. This is similar to a key that only opens a lock. The diversities of protein structures determine the their versatile functions
Two amino acids are stripped of a water molecule to form a peptide bond linking them together. The third, fourth until nth amino acid are attached to the end of peptide chain in the same way. They are similar to the letters in a word; if the letters are arranged differently, the words will be different. No matter how long a peptide is, it always has an amino or carboxyl group at its two ends. The end containing carboxyl group is called the C-terminal and the end containing amino group is called the N-terminal. The peptide bond is covalent bond whose connection is very strong.
Polypeptide chains form secondary structures due to the presence of hydrogen bonds. These hydrogen bonds do not come from side groups, they come from partially positively charged hydrogen atoms and partially negatively charged oxygen atoms on the peptide bond (-CO-NH-). The α helix: some regions or the whole peptide forms a left-handed or right-handed helix structure. Β pleated sheet: peptide arranged parallel to each other form a folded paper sheet through hydrogen bonds. (Two different peptides or different segments of the same peptide)
Polypeptides that have formed a secondary structure bend, fold or coil to create a more complex three-dimensional structure. These factors contribute to the complex tertiary structure: hydrophobic interaction, hydrogen bond, ionic bond and disulfide bond.
Hydrophobic interaction: hydrophobic groups on the peptide chain are clustered in the core of protein to avoid water molecules. The hydrophilic groups are oriented to the outside to form hydrogen bonds with water.
Hydrogen bond: The hydrogen bonds that produce the tertiary structure of proteins come from the side groups of amino acids. The oxygen and hydrogen atoms are attracted to each other because they have partial opposite charges.
Ionic bond: Acidic amino acids and basic amino acids are attracted to each other because they have opposite charges. They have integral opposite charges, so these bonds are stronger than hydrogen bonds.
Disulfide bond: Two cysteines will form a disulfide bond to join different regions of peptide together, result in the peptide chain fold.
Some proteins are composed of multiple peptide chains. These peptide chains with a tertiary structure are called subunits, and they are linked together by van der Waals forces, hydrogen bonds and ionic bonds.