Liu3304_fall2023_lecture_4

Chapter Overview

Chapter 4: Amino Acids

Key Topics:

• Amino Acid Structure:

  • Amino acids are organic compounds vital for life that serve as the building blocks for proteins. They can be visualized as individual Lego pieces that can combine in various ways to form intricate structures.

  • Basic Structure: Each amino acid contains a central carbon (C) atom, an amino group (NH3+), a carboxyl group (COO-), and a unique side chain (R group) that distinguishes each amino acid from others. This side chain contributes to the amino acids' chemical properties and functions.

• Peptide Bonds:

  • Peptide bonds are formed between amino acids via a condensation reaction, where the carboxyl group of one amino acid reacts with the amino group of another, releasing a molecule of water in the process. This linkage is crucial for creating dipeptides, polypeptides, and ultimately larger proteins.

• Classification and Characteristics:

  • Amino acids can be classified into several categories based on their side chains and overall charge:

    • Negative Charge (Acidic): Aspartic acid (Asp, D) and Glutamic acid (Glu, E).

    • Positive Charge (Basic): Lysine (Lys, K), Arginine (Arg, R), and Histidine (His, H).

    • Nonpolar Amino Acids: Include Glycine (Gly, G), Alanine (Ala, A), Valine (Val, V), Leucine (Leu, L), Isoleucine (Ile, I), Methionine (Met, M), Proline (Pro, P), Phenylalanine (Phe, F), and Tryptophan (Trp, W).

    • Polar Amino Acids: Include Serine (Ser, S), Threonine (Thr, T), Asparagine (Asn, N), Glutamine (Gln, Q), Tyrosine (Tyr, Y), and Cysteine (Cys, C).

• Amino Acid Nomenclature:

  • The nomenclature of amino acids often utilizes Greek letters to denote the specific carbon atoms located within the side chains. For example, in Lysine's side chain, the amino group positioned at the terminal end is referred to as Ne, whereas the carboxylic carbon in Glutamic acid is labeled as d. This systematic naming is essential for clarity in amino acid sequences.

• Representation of Amino Acids:

  • Various models exist to represent the structures of amino acids, including line diagrams, stick models, ball-and-stick models, and CPK (space-filling) models, each providing distinct visual insights into molecular geometry. The "CPK" model honors the chemists Corey, Pauling, and Koltun for their contributions to molecular modeling.

• Acid-Base Properties and pKa:

  • The pKa values of amino acids are fundamental for understanding their acid-base properties, influencing how they interact in biological systems. At low pH levels, amino acids typically exist in their protonated state, becoming positively charged due to the addition of protons to the amino group. Conversely, at elevated pH levels, they can lose protons from their carboxyl groups, leading to a neutral or even negative charge. This pH-dependent behavior is crucial for amino acid function in proteins and enzyme activities.

• Isoelectric Point (pI):

  • The isoelectric point (pI) is the specific pH at which an amino acid carries no net charge. To calculate the pI, especially for amino acids with two ionizable groups, the formula 0.5(pK1 + pK2) can be used. It’s important to note that if a side chain can also be ionizable, its pK must be considered in the overall pI calculation.

  • Example Calculations for pI:

    • For Aspartic Acid: pI = 0.5(2.20 + 3.90) = 3.05.

    • For Lysine: pI = 0.5(10.54 + 9.4) = 9.97.

• Disulfide Bonds:

  • Disulfide bonds are formed through the oxidation of the thiol (-SH) groups of two cysteine residues, leading to covalent S-S linkages that provide significant structural stability to proteins. These bonds play a vital role in maintaining the integrity of protein structures, influencing folding and function, and are also involved in biological processes such as hair treatments.

• Protein Sequences and Nomenclature:

  • The sequences of amino acids in proteins are conventionally written from the N-terminus to the C-terminus, ensuring clarity and understanding. Standard abbreviations and naming conventions are crucial to facilitating discussions on polypeptide sequences. For example, the sequence "Lys-Cys-Ala-Thr" indicates the order in which these amino acids are linked in a polypeptide chain.

Exam Preparation Strategies:

• To excel in the exam, thoroughly review Chapter 4 content, ensuring a solid grasp of both structural and functional properties of amino acids.

• Solve practice problems in the textbook related to amino acid pKa and pI calculations to enhance understanding and readiness for the midterm examination.