Introduction to Biochemistry: Amino Acids and Proteins

Amino Acids: The Alphabet of Biochemistry

  • Amino acids serve as the fundamental building blocks in biochemistry, often referred to as the "alphabet of biochemistry."
  • There are 20 different amino acids essential for biological functions.

Diseases Related to Amino Acids

  • Many diseases are associated with amino acid deficiencies.
  • Proteins, which are vital for bodily functions, are coded by DNA.
    • Genetic mutations can lead to enzymes either lacking or having an excess of amino acids, resulting in malfunctions.
  • Understanding amino acids and their role in proteins is crucial for studying health and diseases.

Structure of Amino Acids

General Construction

  • Amino acids consist of three main parts:
    1. Front End (Amine Function):
    • This is the amine functional group.
    • It contains a nitrogen atom bonded to three hydrogen atoms (–NH₃⁺).
    1. Tail End (Carboxylic Acid):
    • This end contains the carboxylic acid group which exists as a carboxylate ion (–COO⁻) when deprotonated.
    1. Side Chain (R group):
    • Located between the amine group and carboxylate ion.
    • The R group varies among the 20 amino acids, distinguishing one amino acid from another.
    • All alpha carbons possess a hydrogen atom attached to them.
  • Notably, some side chains can also have acidic or amino groups, impacting the amino acid's properties.

Essential Amino Acids

  • Essential amino acids must be obtained through the diet because the body cannot synthesize them.
  • Amino acids can be categorized into essential and non-essential:
    • Essential Amino Acids: Cannot be produced by the body; must be ingested.
    • Non-essential Amino Acids: Can be synthesized from other substances or amino acids.
  • A vegetarian or vegan diet must ensure the intake of essential amino acids through plant sources (e.g., legumes, beans).

Amino Acids: Memorization of Structures and Classifications

  • Students should memorize the structures of the 20 amino acids, focusing on the side chains as they differ.
  • Abbreviations:
    • Three-letter: e.g., Gly for Glycine, Ala for Alanine.
    • One-letter abbreviations are less intuitive and are not required for memorization.
  • Categorization:
    • Nonpolar Side Chains: Group of amino acids with side chains that are hydrophobic.
    • Polar Side Chains: Divided into three groups:
    • Polar Acidic: Contain a carboxylic acid group.
    • Polar Basic: Contain amino groups.
    • Polar Neutral: Do not fit into the other categories.

Ions Formed by Amino Acids

  • Amino acids can exist as zwitterions in solution.
    • Zwitterions have both positive and negative charges within the same molecule.
  • The typical pH of biological fluids is approximately 7.4 (neutral):
    • At pH < 7: The amino end is protonated and carries a positive charge while the carboxyl end is neutral.
    • At pH = 7: The amino group carries a positive charge; the carboxyl group becomes a carboxylate ion with a negative charge.
    • At pH > 7: The amino group becomes neutral while the carboxylate retains a negative charge.

Chirality of Amino Acids

  • All amino acids, except glycine, are chiral, meaning they have four different groups attached to their alpha carbon.
  • Amino acids can exist in two forms: D and L isomers.
    • L-amino acids: Naturally occurring forms in proteins.
    • D-amino acids: Rarely found in nature.
  • The chirality matters due to enzyme specificity: only L-amino acids are used in proteins, with D-amino acids causing dysfunction.

Proteins and their Formation

  • Proteins are polymers of amino acids formed by linking them together through peptide bonds.
    • The bond formed between the carboxyl group of one amino acid and the amino group of another through dehydration synthesis (removal of water) is called a peptide bond.
    • Amidation is the process of forming these bonds, which is a special case of dehydration synthesis.
    • Hydrolysis is the reverse process and involves the addition of water to break peptide bonds.
  • Dipeptides: Formed from two amino acids; examples include aspartame, a synthetic sweetener.
  • Polypeptides: Longer chains of amino acids just like polysaccharides but with amino acids as the monomers.

Nonbonded Ends of Peptide Chains

  • Each peptide or protein has two ends:
    • N-terminus: The amino end of the chain.
    • C-terminus: The carboxyl end of the chain.
  • Proteins are written and sequenced from the N-terminus to the C-terminus.

Levels of Protein Structure

Primary Structure

  • The primary structure of proteins is defined by the exact linear sequence of amino acids.
    • Only covalent bonds (peptide bonds) determine this level.

Secondary Structure

  • Secondary structures arise due to hydrogen bonding between the amide groups in the polypeptide backbone, leading to the formation of alpha helices and beta sheets.

Tertiary Structure

  • The tertiary structure involves further folding and three-dimensional organization of the polypeptide based on interactions between the side chains, determined by various intermolecular forces (e.g. hydrogen bonds, ionic bonds, hydrophobic interactions).

Summary Points and Recap

  • Understanding amino acids is fundamental to biochemistry, and knowledge of their structures, functions, and roles in proteins is critical for comprehending biological processes and diseases.
  • Amino acids must be understood not just in isolation but as part of the larger picture involving protein structure and function, interactions, and their implications for health and dietary requirements.