Lecture 3, Biochemistry amino acids

Lecture Overview

• Course: BIOCH-521 - Lecture 3

• Topic: Amino Acids

Lecture Topics

1. Review of Functional Groups

2. Introduction to amino acids – the building blocks of proteins

3. Descriptions and categories of the 20 amino acids that build proteins

4. Essential vs. non-essential amino acids

Review of Functional Groups

• Functional Groups: Chemical moieties that impart specific properties to compounds.

  • Hydrophobic: Superficial dislike of water.

  • Aromatic Compounds: Hydrocarbons structured in rings with multiple double bonds.

• Examples:

  • Aliphatic Hydrocarbon Chains: R-CH3 (e.g., Alanine)

  • Aromatic: Structure including phenyl (e.g., Phenylalanine)

  • Hydroxyl: R-OH (e.g., Ethanol)

Functions of Amino Acids

• Amino acids are the fundamental units of proteins.

• Roles of Proteins:

  • Catalyst for biochemical reactions (enzymes)

  • Structural support

  • Cell signaling (hormones)

  • Immune response (antibodies)

  • Motion (muscle proteins)

• Proteins Structure: Determined by the amino acid sequence; structure dictates function.

Chemical Structure of Amino Acids

• General Structure: Central alpha carbon (Cα) connected to four groups:

  1. Amino group (NH2)

  2. Carboxylic acid group (COOH)

  3. Hydrogen atom (H)

  4. R-group (side chain)

• Distinct R-groups differentiate each amino acid.

Chirality of Amino Acids

• Amino acids are chiral; they have asymmetric centers due to the presence of four different groups.

• Only L-isomers are utilized in protein synthesis on Earth.

Charge Properties of Amino Acids

• At physiological pH (~7), amino acids exist as zwitterions (both positive and negative charges).

• Protonation: Amino and carboxylic groups can gain protons, impacting charge balance.

Categories of Amino Acids

• There are 20 amino acids in total, grouped into:

  1. Hydrophobic Amino Acids (9 amino acids with non-polar R-groups)

  2. Polar Amino Acids (6 amino acids with neutral polar R-groups at pH 7)

  3. Positively Charged Amino Acids (3 amino acids)

  4. Negatively Charged Amino Acids (2 amino acids)

Hydrophobic Amino Acids Overview

• Aliphatic Side Chains: 7 amino acids with simple aliphatic side chains.

• Aromatic Side Chains: 2 amino acids characterized by ring structures (e.g., phenylalanine).

Polar, Neutral Amino Acids

• Description: 6 amino acids with neutral polar side chains; include functional groups like hydroxyl and amide.

Charged Amino Acids

• Positively Charged Amino Acids: 3 amino acids having positive charges due to R-groups at pH 7.

• Negatively Charged Amino Acids: Only 2 amino acids are characterized by negative charges.

Ionizable Side Chains

• Determines the charge at physiological pH based on pKa values:

  • pKa < 7: Group is predominantly in basic form.

  • pKa = 7: Balanced presence of both anionic/cationic forms.

Essential vs. Non-Essential Amino Acids

• Essential Amino Acids: Must be obtained through diet (e.g., histidine, isoleucine, leucine).

• Non-Essential Amino Acids: Can be synthesized in the body (e.g., alanine, glycine).

Summary Points

1. Amino acids are the building blocks of proteins.

2. Understand the amino acid backbone and its charge state at different pH levels.

3. Memorize structures of each amino acid alongside their corresponding codes (3-letter/1-letter).

4. Recognize characteristics (hydrophobicity, polarity, charge) of each amino acid.