BackProteins: Structure, Function, and Regulation (Molecular Biology of the Cell, Ch. 3)
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Proteins: Structure, Function, and Regulation
Amino Acids
Proteins are polymers made from 20 different amino acids, each encoded by DNA. All amino acids share a common backbone but differ in their side chains (R groups), which determine their properties and functions.
Definition: Amino acids are organic molecules with a central (α) carbon atom bonded to an amino group (–NH2), a carboxyl group (–COOH), a hydrogen atom, and a variable side chain (R group).
Peptide Bond: Amino acids are joined by peptide bonds, formed between the amino group of one amino acid and the carboxyl group of another, releasing water (a condensation reaction).
Genetic Code: The sequence of amino acids in a protein is determined by the sequence of codons in DNA.
Side Chains: The R group (side chain) varies among amino acids and determines their chemical nature (polar, nonpolar, charged, etc.).
Example: Glycine (Gly, G) has a hydrogen as its side chain, making it the simplest amino acid.
Polypeptide Chain
A polypeptide chain is a linear sequence of amino acids linked by peptide bonds. The chain has directionality, with an N-terminus (amino end) and a C-terminus (carboxyl end).
Backbone: The repeating sequence of –N–Cα–C– forms the polypeptide backbone.
Side Chains: Project from the backbone and interact to determine protein structure and function.
Example: A polypeptide containing methionine, aspartic acid, leucine, and tyrosine demonstrates the diversity of side chains.
Amino Acid Classification
Amino acids are grouped based on the properties of their side chains (R groups). Each amino acid is assigned both a three-letter and a one-letter abbreviation.
Polar Amino Acids: Side chains can form hydrogen bonds; may be charged (acidic or basic) or uncharged.
Nonpolar Amino Acids: Side chains are hydrophobic and tend to cluster in the protein interior.
Amino Acid | Abbreviation | Side Chain Property |
|---|---|---|
Aspartic acid | Asp (D) | Negative (acidic, polar) |
Glutamic acid | Glu (E) | Negative (acidic, polar) |
Arginine | Arg (R) | Positive (basic, polar) |
Lysine | Lys (K) | Positive (basic, polar) |
Histidine | His (H) | Positive (basic, polar) |
Asparagine | Asn (N) | Uncharged polar |
Glutamine | Gln (Q) | Uncharged polar |
Serine | Ser (S) | Uncharged polar |
Threonine | Thr (T) | Uncharged polar |
Tyrosine | Tyr (Y) | Uncharged polar |
Alanine | Ala (A) | Nonpolar |
Glycine | Gly (G) | Nonpolar |
Valine | Val (V) | Nonpolar |
Leucine | Leu (L) | Nonpolar |
Isoleucine | Ile (I) | Nonpolar |
Proline | Pro (P) | Nonpolar |
Phenylalanine | Phe (F) | Nonpolar |
Methionine | Met (M) | Nonpolar |
Tryptophan | Trp (W) | Nonpolar |
Cysteine | Cys (C) | Nonpolar |
Additional info: Table entries inferred from standard amino acid properties.
Bonds Within Proteins
Protein structure is stabilized by several types of bonds and interactions between amino acid side chains and the backbone.
Electrostatic Attractions: Occur between charged side chains (e.g., lysine and glutamate).
Hydrogen Bonds: Form between polar groups, including backbone atoms and side chains.
Van der Waals Attractions: Weak interactions between nonpolar side chains (e.g., valine and alanine).
Disulfide Bonds: Covalent bonds between cysteine residues, stabilizing protein structure (not shown in this set but important for tertiary structure).
Example: Hydrogen bonds between backbone carbonyl and amide groups stabilize α-helices and β-sheets.
