Bio350 lecture 2

Amino Acids: Abbreviations, Structure, and Building Blocks

  • Amino acids are the building blocks of proteins. Each amino acid has:

    • a long name, a three-letter abbreviation, and a one-letter abbreviation
    • a common backbone with a unique side chain (R-group)

  • One-letter abbreviations can be problematic because many amino acids start with the same letter, so some letters are reused with different meanings (e.g., Tyrosine = Y, Tryptophan = W). Overall: every amino acid has:

    • long name, three-letter abbreviation, and one-letter abbreviation.

  • Examples from the transcript:

    • Histidine: three-letter = His, one-letter = H
    • Aspartic acid: three-letter = Asp, one-letter = D (A isn’t used here because Alanine already uses A)
    • Leucine: three-letter = Leu, one-letter = L
    • Tyrosine: three-letter = Tyr, one-letter = Y
    • The three-letter abbreviation for Lysine is Lys; one-letter = K

  • Structural representation of an amino acid:

    • amine group (–NH2) and carboxyl group (–COOH)
    • a central carbon (the α-carbon) with a hydrogen and a side chain (R)
    • backbone: N–Cα–C, with the amino group on the left and the carboxyl group on the right

  • The amino group and carboxyl group are functional groups essential to reactivity:

    • amino group: –NH2 (often shown as –NH3+ at physiological pH)
    • carboxyl group: –COOH (often deprotonated to –COO− at physiological pH)

  • There are 20 standard amino acid side chains (R-groups) that determine the chemistry and function of each amino acid.

  • The basic unit for a protein is a single amino acid; proteins are formed by linking many amino acids together via peptide bonds.

  • Dehydration synthesis (condensation) to form peptide bonds:

    • When two amino acids come together, the carboxyl carbon of amino acid 1 bonds to the amino nitrogen of amino acid 2, releasing a molecule of water (H2O).
    • General reaction:
      extAminoacid<em>1 + Amino acid</em>2→Dipeptide+H2Oext{Amino acid}<em>1\ + \, \text{Amino acid}</em>2 \rightarrow \text{Dipeptide} + \mathrm{H_2O}
    • The resulting linkage is called a peptide bond (–C(=O)–N–C). This is the backbone linkage that repeats along the chain: NCC (N–Cα–C) repeating units with side chains branching off the Cα.

  • Primary structure (primary sequence):

    • The linear sequence of amino acids in a protein.
    • Example from the transcript: the four-amino-acid protein has the primary sequence HDLYC.
    • The sequence is often written with a dash between residues; for example, H–D–L–Y–C, and the terminus positions are:
    • N-terminus (amino terminus): the start of the chain where translation begins
    • C-terminus (carboxyl terminus): the end of the chain where translation ends
    • Translation proceeds from N-terminus to C-terminus in the ribosome.

  • Protein synthesis location:

    • Protein synthesis occurs on ribosomes, which are cellular structures in the cytoplasm (sometimes associated with the endoplasmic reticulum).
    • Ribosomes are the molecular machines that manufacture proteins by linking amino acids in the order dictated by mRNA.

  • The backbone vs side chains:

    • Backbone (N–Cα–C) contains the amide bonds that form peptide linkages.
    • Side chains (R-groups) extend from the Cα and determine the chemical properties of each amino acid.
    • Secondary structure (alpha-helix, beta-sheet) is determined by interactions along the NCC backbone and hydrogen bonding between backbone atoms, not by side chains.

  • Secondary structure (brief overview):

    • Alpha helix: a right-handed coil stabilized by hydrogen bonds between the backbone N–H and C=O groups four residues apart (i to i+4).
    • Beta sheet: beta strands connected laterally by at least two or more hydrogen bonds forming a sheet-like array; strands can run parallel or antiparallel.
    • These structures arise from hydrogen bonding along the NCC backbone and do not involve side-chain interactions directly.

  • Tertiary structure (three-dimensional folding):

    • The overall 3D shape of a single polypeptide chain.
    • Determined by numerous hydrogen bonds, ionic interactions, hydrophobic effects, and van der Waals forces involving side chains (R-groups).
    • Hydrophobic (lipid-soluble) side chains tend to bury in the protein interior; hydrophilic (water-soluble) side chains tend to face the exterior in aqueous environments.
    • Disulfide bridges (covalent S–S bonds) can stabilize the tertiary structure; formed between cysteine residues.
    • Cysteine contains sulfur in a thiol group (–SH); two cysteines can form a disulfide bond: 2 R−CH<em>2−SH→R−CH</em>2−S−S−CH2−R+2 H++2 e−2\,\mathrm{R-CH<em>2-SH} \rightarrow \mathrm{R-CH</em>2-S-S-CH_2-R} + 2\,H^+ + 2\,e^-
    • Some proteins have a “domain” structure: distinct regions within a single polypeptide with specific functions; domains can act as functional units (e.g., an active site in enzymes).

  • Quaternary structure (fourth level):

    • Assembly of multiple polypeptide subunits into a functional protein complex.
    • Subunits are individual polypeptide chains within the complex.
    • Examples:
    • Homodimer: two identical subunits (e.g., two identical tertiary structures) come together.
    • Heterodimer: two different subunits come together.
    • Tetramer: four subunits; octamer: eight subunits.