Amino Acids, Proteins, and Enzymes: Primary Structure and Essential Amino Acids

Chapter 16: Amino Acids, Proteins, and Enzymes

16.2 Proteins: Primary Structure

The primary structure of proteins refers to the specific sequence of amino acids linked together by peptide bonds. This sequence determines the protein's unique properties and biological function.

• Peptide Bond: An amide bond formed when the carboxyl group (COO-) of one amino acid reacts with the amino group (NH3+) of another amino acid.

• Peptide: A molecule formed by linking two or more amino acids via peptide bonds.

• Formation Reaction: $\text{Amino Acid}_1 + \text{Amino Acid}_2 \rightarrow \text{Dipeptide} + H_2O$

• Example: The peptide bond in glycylalanine (Gly-Ala) links glycine and alanine.

Formation and Classification of Peptides

Peptides are classified based on the number of amino acids they contain:

• Dipeptide: Contains two amino acids.

• Tripeptide: Contains three amino acids.

• Tetrapeptide: Contains four amino acids.

• Polypeptide: Contains many amino acids; proteins are polypeptides with 50 or more amino acids.

Drawing and Naming Peptides

Peptides are named using the three-letter abbreviations of their constituent amino acids, listed from the N-terminus (left) to the C-terminus (right).

• Example: A peptide made of alanine, glycine, and serine is named Ala-Gly-Ser or Alanylglycylserine.

• Drawing Peptides: To draw a peptide, connect the carboxyl group of one amino acid to the amino group of the next, removing a water molecule for each bond formed.

Sample Problem: Drawing a Dipeptide (Ser-Thr)

• Step 1: Write the structures of serine and threonine.

• Step 2: Remove the OH from the carboxyl group of serine and two H from the amino group of threonine.

• Step 3: Connect the two amino acids via a peptide bond.

• Result: The dipeptide Ser-Thr is formed.

Sample Problem: Drawing a Tripeptide (Gly-Ser-Met)

1. Draw the structure for each amino acid in the peptide, starting with the N-terminus.

2. Remove the O atom from the carboxyl group of the N-terminus and two H atoms from the ammonium group in the adjacent amino acid. Repeat for each bond.

3. Connect the amino acids using peptide bonds.

Identifying Amino Acids in Peptides

Peptides can be identified by their three-letter abbreviations or full names. The order of amino acids is crucial for function.

• Example: Alanylleucylcysteinylmethionine (Ala-Leu-Cys-Met) is a tetrapeptide with alanine, leucine, cysteine, and methionine in sequence.

• Learning Check: Given two glycines and one alanine, possible tripeptides are:

  • glycylglycylalanine (Gly-Gly-Ala)

  • glycylalanylglycine (Gly-Ala-Gly)

  • alanylglycylglycine (Ala-Gly-Gly)

Chemistry Link to Health: Essential Amino Acids

Of the 20 amino acids used to build proteins in the human body, only 11 can be synthesized internally. The remaining 9 are essential amino acids and must be obtained from dietary sources.

Essential Amino Acid	Abbreviation
Histidine	His, H
Isoleucine	Ile, I
Leucine	Leu, L
Lysine	Lys, K
Methionine	Met, M
Phenylalanine	Phe, F
Threonine	Thr, T
Tryptophan	Trp, W
Valine	Val, V

• Complete Proteins: Foods such as eggs, milk, meat, and fish contain all essential amino acids.

• Incomplete Proteins: Plant sources like grains, beans, and nuts may lack one or more essential amino acids.

Primary Structure of Proteins

The primary structure of a protein is the unique sequence of amino acids in its polypeptide chain. This sequence is critical for the protein's biological activity.

• Example: The sequence Ala-Leu-Cys-Met forms a specific polypeptide.

• Importance: Even if the same amino acids are present, only the correct sequence yields the desired biological function. For example, the tripeptide Glu-His-Pro acts as a thyroid hormone, but other sequences of these amino acids do not.

Summary Table: Peptide Classification

Number of Amino Acids	Peptide Type
2	Dipeptide
3	Tripeptide
4	Tetrapeptide
50 or more	Protein (Polypeptide)

Key Equations

• Peptide Bond Formation: $\text{Amino Acid}_1 + \text{Amino Acid}_2 \rightarrow \text{Dipeptide} + H_2O$

Additional info:

• The N-terminus of a peptide is the end with a free amino group; the C-terminus is the end with a free carboxyl group.

• Peptide bonds are covalent and form the backbone of protein structure.

• Proteins are essential for biological processes such as catalysis (enzymes), structure, transport, and signaling.