Amino Acids: Structure and Properties

Overview of the 20 Common Amino Acids

Amino acids are the building blocks of proteins, each with a unique side chain (R group) that determines its chemical properties. Understanding their structures and classifications is essential for biochemistry.

• Classification: Amino acids are categorized as non-polar, polar, aromatic, acidic, or basic based on their side chains.

• Stereochemistry: Most amino acids (except glycine) are chiral, existing as L- and D- enantiomers. Proteins are composed of L-amino acids.

• One-letter and three-letter codes: Each amino acid has a standard abbreviation (e.g., Gly for glycine, G).

• Drawing and naming: Students should be able to draw and name all 20 amino acids.

Example: Phenylalanine (Phe, F) is an aromatic, non-polar amino acid.

Ionization and Isoelectric Point (pI)

Amino acids can exist in different ionization states depending on pH. The isoelectric point (pI) is the pH at which the amino acid has no net charge.

• Ionizable groups: Amino acids have at least two ionizable groups (amino and carboxyl); some have ionizable side chains.

• Calculating pI: For amino acids without ionizable side chains,

Example: Glycine has a pI of approximately 6.0.

Peptides and Protein Structure

Peptide Bond and Its Properties

The peptide bond links amino acids in a protein, forming the backbone of the polypeptide chain.

• Definition: A peptide bond is a covalent bond between the carboxyl group of one amino acid and the amino group of another.

• Planarity: Peptide bonds are planar due to partial double-bond character, restricting rotation.

• Contribution to structure: Peptide bonds and their geometry are crucial for protein secondary structure.

Example: The backbone of a protein consists of repeating N–Cα–C units.

Primary Structure: N-terminus and C-terminus

The primary structure of a protein is its unique sequence of amino acids, starting at the N-terminus and ending at the C-terminus.

• N-terminus: The end of the polypeptide with a free amino group.

• C-terminus: The end with a free carboxyl group.

Example: Insulin has a specific amino acid sequence that determines its function.

Genetic Code and Protein Synthesis

Translating the Genetic Code

Proteins are synthesized based on genetic information encoded in DNA and RNA.

• Codons: Triplets of nucleotides in mRNA that specify amino acids.

• Open Reading Frame (ORF): A continuous stretch of codons that begins with a start codon and ends with a stop codon.

• Gene recognition: Identifying ORFs is essential for gene annotation and protein prediction.

Example: The codon AUG codes for methionine and signals the start of translation.

Protein Purification Techniques

Size Exclusion Chromatography

This technique separates proteins based on their size by passing them through a column filled with porous beads.

• Principle: Larger proteins elute first because they cannot enter the pores; smaller proteins elute later.

• Application: Used to estimate molecular weight and purify proteins.

Example: Separation of hemoglobin from smaller peptides.

Ion Exchange Chromatography

Proteins are separated based on their net charge by passing them through a column with charged resin.

• Cation exchange: Binds positively charged proteins.

• Anion exchange: Binds negatively charged proteins.

• Elution: Proteins are eluted by increasing salt concentration or changing pH.

Example: Purification of ribonuclease using cation exchange chromatography.

SDS-PAGE (Sodium Dodecyl Sulfate Polyacrylamide Gel Electrophoresis)

SDS-PAGE is an analytical technique used to separate proteins by molecular weight.

• Principle: Proteins are denatured and coated with SDS, giving them a uniform negative charge.

• Separation: Proteins migrate through a polyacrylamide gel; smaller proteins move faster.

Example: Determining the purity and size of a recombinant protein.

Affinity Chromatography

This method separates proteins based on specific binding interactions with a ligand attached to the column matrix.

• Principle: Only proteins with high affinity for the ligand are retained; others are washed away.

• Application: Used for purifying enzymes, antibodies, or tagged proteins.

Example: Purification of His-tagged proteins using nickel affinity columns.

Key Biochemical Terms and Concepts

Chirality

Chiral centers are carbon atoms bonded to four different groups, resulting in non-superimposable mirror images (enantiomers).

• Importance: Chirality affects the biological activity of amino acids and drugs.

Example: L-alanine vs. D-alanine.

Fischer Projection

A Fischer projection is a two-dimensional representation of a molecule, commonly used for carbohydrates and amino acids.

• Horizontal lines: Represent bonds projecting out of the plane.

• Vertical lines: Represent bonds going behind the plane.

Example: Representation of D-glucose.

Zwitterion

A zwitterion is a molecule with both positive and negative charges but is overall electrically neutral. Amino acids exist as zwitterions at physiological pH.

• Structure:

Example: Glycine at pH 7.

Conservative vs. Non-conservative Mutations

• Conservative mutation: Changes the amino acid to one with similar properties (size, charge, polarity).

• Non-conservative mutation: Changes the amino acid to one with different properties, potentially affecting protein function.

Example: Glutamate to aspartate (conservative); glutamate to lysine (non-conservative).

Main Chain and Amino Acid Residue

• Main chain: The backbone of a peptide chain, excluding side chains.

• Amino acid residue: An amino acid within a chain, after condensation.

Genetic Terms

• Coding strand: The DNA strand with the same sequence as mRNA (except T for U).

• Non-coding strand: The template strand used for RNA synthesis.

• Open Reading Frame (ORF): A DNA sequence that can be translated into a protein.

Summary Table: Protein Purification Techniques

Additional info: Some explanations and examples have been expanded for clarity and completeness, based on standard biochemistry curriculum.