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

Proteins: Primary Structure

Peptide Bonds and Peptide Formation

The primary structure of proteins refers to the specific sequence of amino acids in a polypeptide chain, held together by peptide bonds. Understanding how these bonds form is fundamental to biochemistry and protein function.

• Peptide bond: An amide bond formed between the carboxylate group (--COO-) of one amino acid and the amino group (--NH3+) of the next amino acid.

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

Equation for peptide bond formation:

$\text{Amino acid}_1 + \text{Amino acid}_2 \rightarrow \text{Dipeptide} + H_2O$

• Dipeptide: Formed from two amino acids.

• Tripeptide: Formed from three amino acids.

• Tetrapeptide: Formed from four amino acids.

Example: The dipeptide Ser-Thr is formed by linking serine and threonine through a peptide bond.

Naming Peptides

Peptides are named by listing the amino acids in order from the N-terminus (amino end) to the C-terminus (carboxyl end), using either full names or standard three-letter abbreviations.

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

N-terminus	Middle	C-terminus
Alanine (Ala)	Glycine (Gly)	Serine (Ser)

Identifying Amino Acids in Peptides

Given a peptide's name or abbreviation, you can identify the sequence of amino acids it contains.

• Example: Alanylleucylcysteinylmethionine (Ala-Leu-Cys-Met) is a tetrapeptide with the following sequence:

Position	Amino Acid
1	Alanine (Ala)
2	Leucine (Leu)
3	Cysteine (Cys)
4	Methionine (Met)

Chemistry Link to Health: Essential Amino Acids

Essential vs. Non-Essential Amino Acids

Of the 20 amino acids used to build proteins in the human body:

• 11 can be synthesized by the body (non-essential amino acids).

• 9 are essential amino acids and must be obtained from dietary proteins.

Table: Essential Amino Acids for Adults

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 (e.g., eggs, milk, meat, fish) contain all essential amino acids. Incomplete proteins (e.g., grains, beans, nuts) lack one or more essential amino acids.

Primary Structure of Proteins

Definition and Importance

A protein is a polypeptide of 50 or more amino acids with biological activity. The primary structure is the unique sequence of amino acids in a protein, which determines its function and properties.

• The sequence is held together by peptide bonds.

• Even a small change in the sequence can alter the protein's function.

Example: The hormone with sequence Glu-His-Pro stimulates thyroxin release. Other sequences of these three amino acids do not have the same activity.

Examples and Practice Problems

• Tripeptides from two glycines and one alanine:

Name	Abbreviation
Glycylglycylalanine	Gly-Gly-Ala
Glycylalanylglycine	Gly-Ala-Gly
Alanylglycylglycine	Ala-Gly-Gly

• Identifying N-terminus and C-terminus: In a peptide with abbreviation Pro-His-Met, the N-terminus is proline, and the C-terminus is methionine.

Drawing Peptide Structures

To draw a peptide:

1. Write the structure for each amino acid in the sequence, starting from the N-terminus.

2. Remove the O atom from the carboxyl group of the N-terminus and two H atoms from the ammonium group of the adjacent amino acid to form a peptide bond.

3. Repeat until the C-terminus is reached, connecting all amino acids with peptide bonds.

Example: Drawing the tripeptide Gly-Ser-Met involves connecting glycine, serine, and methionine in order, forming peptide bonds between each pair.

Example: Drawing the dipeptide Phe-Thr (phenylalanine-threonine) involves linking the carboxyl group of phenylalanine to the amino group of threonine.

Additional info: The primary structure is the foundation for higher levels of protein structure (secondary, tertiary, quaternary), which determine the protein's 3D shape and biological function.