TChem_Chapter_14__The_Building_Blocks_of_Life

ThanatoChemistry

Chapter 14: The Building Blocks of Life

Chapter 14 To-Do’s

  • Understand the following key concepts regarding amino acids:
    • Characteristics of Amino Acids
    • Their structure and "personalities"
    • How amino acids are classified
    • Definition of "Zwitterion"
    • Amphoteric Nature of amino acids
    • Utilization as "Buffers"
    • Structure comparisons:
    • Amino Acid vs. Peptide vs. Protein
    • Fibrous vs. Globular Protein
    • Locations of these in the human body
    • Functions of specific proteins in the body (see Chart 14.2)
    • Structural comparisons:
    • Primary, Secondary, Tertiary, and Quaternary protein structures
    • Description of Hemoglobin and Myoglobin
    • Composition and location in the body
    • Functions of hemoglobin and myoglobin
    • Definition and methods of Denaturation

Amino Acids

  • Amino acid + amino acid = Protein
    • Known as the "Building Blocks of Life"
    • Composition:
    • 1 Amine Group (Basic)
    • 1 Carboxyl Group (Acidic)
    • Abbreviations with 3 letters:
    • Example: Tryptophan = Trp
  • Alpha-Amino Acids
    • Most important category
    • Amine and carboxyl groups attached to the same Carbon (Alpha-Carbon)
    • The "Magic 20" amino acids include:
    • Unique identity from R-Groups
    • Classified as:
      • NonPolar (Hydrophobic)
      • Polar
      • Acid/Base

Overview of the Twenty Common Amino Acids

  • Amino Acid Chart Key
    • Aliphatic
    • Aromatic
    • Acidic
    • Basic
    • Hydroxylic
    • Sulfur-containing
    • Amidic
    • Non-Essential
    • Essential
  • Chemical Structure, Single Letter, and Three Letter Codes:
    • Glycine (G, Gly)
    • Alanine (A, Ala)
    • Phenylalanine (F, Phe)
    • Lysine (K, Lys)
    • Isoleucine (I, Ile)
    • Leucine (L, Leu)
    • Tryptophan (W, Trp)
    • Tyrosine (Y, Tyr)
    • Aspartic Acid (D, Asp)
    • Glutamic Acid (E, Glu)
    • Proline (P, Pro)
    • Valine (V, Val)
    • Arginine (R, Arg)
    • Histidine (H, His)
    • Serine (S, Ser)
    • Threonine (T, Thr)
    • Cysteine (C, Cys)
    • Methionine (M, Met)
    • Asparagine (N, Asn)
    • Glutamine (Q, Gln)

Zwitterion

  • Zwitterion (Zwitter-ion):
    • Amino acids possess both an alpha amine functional group (+) and an alpha carboxylic acid functional group (-).
    • Capable of existing as both Acid and Base.
    • Some amino acids carry a charge, making them Zwitterions:
    • Exist as a cation and anion simultaneously
    • Highly soluble in water
    • Play a role in determining protein structure
    • Aid in drug delivery to target tissues

Amphoterism

  • Amphoterism (Amphoteric):
    • Amino acids can function as acids or bases, similar to water (H2O).
    • Under different pH conditions:
    • Acidic pH (<7): major form is +ion
    • Basic pH (>7): major form is -ion

Buffers

  • Buffers:
    • Amino acids can act as pseudo-buffers due to their amphoteric nature.
    • A buffer is a mixture of an acid and its conjugate base:
    • Alpha carbonyl group serves as the acid
    • Alpha amino group serves as the conjugate base
    • Buffers resist pH changes by partially absorbing acids or bases.
    • Proteins can also serve as buffers due to their amino acids.

Peptides

  • Peptide Formation:
    • Amino acid + amino acid = Peptide
    • Formed by a peptide bond between the amino group of one amino acid and the carboxyl group of another.
    • Each peptide has
    • N-Terminal (-NH2) at one end
    • C-Terminal (-COOH) at the other end
    • Polypeptide:
    • Long, continuous, unbranched chain with <50 peptide bonds.

Proteins

  • Proteins:
    • Composed of more than 50 peptide links and referred to as "macromolecules."
    • Two categories in the human body:
    • Fibrous Protein:
      • Provides structure to organs, skin, muscles, tendons, and bones.
      • Not water-soluble.
    • Globular Protein:
      • Function as transporters (e.g., hemoglobin, myoglobin, immunoglobulins)
      • Act as biochemical catalysts (enzymes)
      • Water-soluble.

Proteins in the Human Body

  • Proteins are crucial in various bodily functions:
    • Immune System:
    • Antibodies fight invaders.
    • The complement system, activated during infections, consists of 20 protein molecules.
    • Muscle:
    • Actin and myosin enable muscle movement.
    • Myoglobin releases oxygen to muscles; ferritin stores and releases oxygen.
    • Signaling Proteins:
    • Cytokines communicate with other cells.
    • Proteins in the Blood:
    • Hemoglobin transports oxygen.
    • Fibrinogen assists with blood clotting.
    • Albumin maintains liquid levels in blood.
    • Structural Proteins:
    • Contribute to cytoskeleton structure, maintaining cell shape.
    • Keratin (found in skin, hair, nails), collagen (provides strength), elastin (provides flexibility).
    • Enzymes:
    • Aid in digestion and biochemical reactions.

Protein Structure

  • The function of proteins is closely related to their structure, which has four levels:
    1. Primary Protein Structure:
    • The sequence of amino acids forms the "foundation" of the protein.
    • Sulfur bonds between cysteine amino acids create disulfide bridges, which can occur within or between protein chains.
    1. Secondary Protein Structure:
    • Amino acids in the same chain are held together by hydrogen bonds.
    • Structures include alpha-helix and pleated sheet formations.
    1. Tertiary Protein Structure:
    • Combination of primary and secondary structures.
    • Involves hydrogen bonds, electrostatic interactions, disulfide bridges, and interactions between hydrophobic and hydrophilic sides that create bending and folding of the protein.
    1. Quaternary Protein Structure:
    • Interaction between two or more protein chains (subunits).
    • Interactions may include hydrogen bonds and disulfide bridges.

Fibrous Proteins

  • Fibrous Protein:
    • Provide structural support to skin, organs, muscles, tendons, and bones.
    • Most abundant protein type in the body made of repeating amino acid units.
    • Secondary structure is often a helix with numerous cross-links between chains.
    • Hydrophobic side chains protrude from the structure, enhancing stability.
    • Less susceptible to denaturation compared to globular proteins.
    • Example: Collagen - serves as structural "glue"; properties vary (rigid for bone, soft for tendons, intermediate for cartilage).

Hemoglobin & Myoglobin

  • Hemoglobin:
    • Features both tertiary and quaternary structures with 4 globular subunits (2 alpha and 2 beta chains).
    • Each subunit contains 1 heme molecule with an iron atom, binding and transporting oxygen from lungs to tissues and CO2 from tissues to lungs.
  • Myoglobin:
    • Functions similarly to hemoglobin but is found in muscle tissue.
    • Composed of a single protein chain and one heme molecule.

Denaturation

  • Denaturation:
    • Proteins lose their three-dimensional structure without affecting the primary structure.
    • Results in loss of solubility as hydrophobic groups are exposed.
    • Caused by:
    • Heat (e.g., frying an egg)
    • Harsh acid/base conditions (e.g., ceviche)
    • Organic solvents (e.g., ethanol, methanol, acetone).

Putrefaction

  • Putrefaction:
    • Refers to the decomposition and denaturation of proteins and amino acids, occurring after death; it is the 5th stage in the "Stages of Death."