Unit 4: Biomolecules

1. Biomolecules as Building Blocks of Biological Subjects

Biomolecules are organic molecules produced by living organisms that are essential for one or more biological processes, such as cell division, morphogenesis, or development. They are the fundamental building blocks of life.

• Monomers and Polymers: Most large biomolecules (macromolecules) are polymers, which are long chains made of repeating smaller units called monomers.

  • Monomer: A single, relatively simple molecule that can covalently bond with other monomers to form a polymer.
  • Polymer: A large molecule (macromolecule) composed of many repeated subunits (monomers).
  • Polymerization: The process of joining monomers to form a polymer. In biological systems, this is typically a dehydration synthesis (or condensation) reaction, where a molecule of water is removed to form a new bond.
  • Depolymerization (Hydrolysis): The process of breaking down a polymer into monomers by adding a molecule of water.

• The Four Major Classes of Biomolecules:

2. Carbohydrates

Carbohydrates (or saccharides) are the most abundant biomolecules on Earth. Their name comes from their general empirical formula, C_n(H₂O)_n, suggesting they are "hydrates of carbon."

• Functions:
  • Energy Source: The primary source of metabolic energy for cells (e.g., glucose).
  • Energy Storage: Stored as glycogen in animals and starch in plants.
  • Structural Component: Form the cell wall of plants (cellulose) and the exoskeleton of arthropods (chitin).
  • Cell Recognition: Act as molecular markers on cell surfaces.

2.1. Structure of Selected Monosaccharides

Monosaccharides are the simplest form of carbohydrates ("simple sugars") and serve as the monomers for larger carbohydrates. They typically contain 3 to 7 carbon atoms.

Glucose (C₆H₁₂O₆)

• Classification: An aldohexose (an aldose with an aldehyde group and a hexose with six carbon atoms).
• Structure: Exists in both a linear (Fischer projection) and a cyclic (Haworth projection) form. In aqueous solution, the cyclic form is overwhelmingly predominant.
• Cyclic Form: The ring forms when the hydroxyl group on Carbon-5 attacks the aldehyde group on Carbon-1. This creates a new chiral center at C-1, resulting in two anomers:
  • α-Glucose: The hydroxyl (-OH) group on C-1 is on the opposite side of the ring from the CH₂OH group (C-6).
  • β-Glucose: The hydroxyl (-OH) group on C-1 is on the same side of the ring as the CH₂OH group (C-6).
  • This distinction is critical for the structure of polysaccharides.

      Linear (Fischer)           α-Glucose (Haworth)         β-Glucose (Haworth)
         CHO                             H--C--OH                       HO--C--H
         |                               |                              |
      H--C--OH                         H--C--OH                       H--C--OH
         |                               |                              |
      HO--C--H                         HO--C--H                       HO--C--H
         |                               |                              |
      H--C--OH                         H--C--OH                       H--C--OH
         |                               |                              |
      H--C--OH                         H--C                           H--C
         |                               | \  / O                       | \  / O
         CH2OH                           CH2OH                          CH2OH

Fructose (C₆H₁₂O₆)

• Classification: A ketohexose (a ketose with a ketone group and a hexose with six carbons). It is a structural isomer of glucose.
• Structure: Also exists in linear and cyclic forms. The ring is a five-membered ring (a furanose), formed when the hydroxyl on C-5 attacks the ketone on C-2.

2.2. Structure of Selected Disaccharides

Disaccharides are formed when two monosaccharides are joined by a glycosidic bond through a dehydration reaction.

Sucrose (Table Sugar)

• Composition: One molecule of α-Glucose and one molecule of β-Fructose.
• Glycosidic Bond: An α(1→2)β linkage. The bond is between C-1 of glucose and C-2 of fructose.
• Function: The primary form in which sugars are transported in plants.

Maltose (Malt Sugar)

• Composition: Two molecules of α-Glucose.
• Glycosidic Bond: An α(1→4) linkage. The bond is between C-1 of the first glucose and C-4 of the second glucose.
• Function: An intermediate product of starch digestion.

2.3. Structure of Selected Polysaccharides

Polysaccharides are long polymers of monosaccharides linked by glycosidic bonds.

Starch

• Function: The primary energy storage polysaccharide in plants.
• Monomer: α-Glucose.
• Structure: A mixture of two polymers:
  1. Amylose: A linear, unbranched chain of α-glucose units joined by α(1→4) glycosidic bonds. This structure causes it to form a loose helix.
  2. Amylopectin: A branched polymer of α-glucose. The main chain has α(1→4) linkages, with branch points created by α(1→6) linkages occurring every 24-30 residues. This branching allows for rapid glucose release.

Cellulose

• Function: The primary structural component of plant cell walls. It is the most abundant organic polymer on Earth.
• Monomer: β-Glucose.
• Structure: A linear, unbranched polymer of β-glucose units joined by β(1→4) glycosidic bonds.
• Key Structural Feature: The β(1→4) linkage causes each glucose monomer to be "flipped" relative to the next. This results in long, straight, rigid chains. These parallel chains can form extensive hydrogen bonds with each other, creating strong, insoluble microfibrils. This property makes cellulose an excellent structural material. Humans cannot digest cellulose because they lack the enzyme to break the β(1→4) bonds.

3. Lipids

Lipids are a diverse group of hydrophobic molecules, meaning they are insoluble in water but soluble in nonpolar organic solvents. They are not true polymers as they are not built from a repeating chain of identical monomers.

• Functions:
  • Long-Term Energy Storage: Fats and oils (triglycerides) store more energy per gram than carbohydrates.
  • Structural Components: Phospholipids and cholesterol are essential components of cell membranes.
  • Insulation & Protection: Adipose tissue (fat) insulates the body and cushions organs.
  • Hormones: Steroid hormones (e.g., testosterone, estrogen) act as chemical messengers.

3.1. Lipid Structure

Fatty Acids

• The fundamental building blocks of many lipids.
• Structure: A long hydrocarbon chain (typically 12-24 carbons) with a terminal carboxyl group (-COOH).
• Types:
  • Saturated Fatty Acids: Contain only carbon-carbon single bonds. The chains are straight and can pack tightly, making them solid at room temperature (e.g., butter, lard).
  • Unsaturated Fatty Acids: Contain one or more carbon-carbon double bonds.
    • The double bonds (usually in a cis configuration) create "kinks" or bends in the chain.
    • These kinks prevent tight packing, making them liquid at room temperature (e.g., olive oil).

Triglycerides (Fats & Oils)

• Structure: Composed of one glycerol molecule and three fatty acid molecules.
• Formation: The fatty acids are attached to the glycerol via ester linkages formed during dehydration synthesis.

Phospholipids

• Structure: Similar to a triglyceride, but one fatty acid is replaced by a phosphate group attached to the third carbon of the glycerol backbone.
• Amphipathic Nature:
  • Hydrophilic Head: The phosphate group and its attachments are polar and charged.
  • Hydrophobic Tails: The two fatty acid chains are nonpolar.
• Function: This dual nature is crucial for their function. In water, they spontaneously self-assemble into a lipid bilayer, forming the basic structure of all biological membranes.

4. Proteins

Proteins are the most functionally diverse macromolecules in living systems. They are polymers of amino acids.

• Functions:
  • Enzymes: Catalyze biochemical reactions.
  • Structural: Provide support (e.g., collagen in connective tissue, keratin in hair and nails).
  • Transport: Carry substances (e.g., hemoglobin transports oxygen).
  • Movement: Contractile proteins (e.g., actin and myosin in muscles).
  • Regulation: Hormones and transcription factors.
  • Defense: Antibodies of the immune system.

4.1. Structure of Protein

The function of a protein is dictated by its complex three-dimensional shape, which is described by four levels of structure.

Primary (1°) Structure

• Definition: The unique, linear sequence of amino acids in a polypeptide chain.
• Bonding: The amino acids are linked by covalent peptide bonds.
• Determination: This sequence is determined by the genetic information encoded in DNA. A change in a single amino acid can alter or destroy protein function.

Secondary (2°) Structure

• Definition: Local, repeating folding patterns of the polypeptide backbone.
• Bonding: Stabilized by hydrogen bonds between the carbonyl oxygen (C=O) and amide hydrogen (N-H) of the peptide backbone, NOT the side chains (R-groups).
• Common Motifs:
  • α-helix: A right-handed coil/spiral structure. Hydrogen bonds form between every fourth amino acid, pulling the backbone into a helix.
  • β-pleated sheet: Two or more segments of the polypeptide chain lie side-by-side. Hydrogen bonds form between these adjacent strands. The strands can be parallel (running in the same direction) or antiparallel (running in opposite directions).

Tertiary (3°) Structure

• Definition: The overall three-dimensional shape of a single polypeptide chain, resulting from interactions between the various side chains (R-groups).
• Bonding and Interactions: A combination of several forces stabilizes the tertiary structure:
  • Hydrophobic Interactions: Nonpolar R-groups tend to cluster in the protein's interior, away from the aqueous environment.
  • Hydrogen Bonds: Between polar R-groups.
  • Ionic Bonds (Salt Bridges): Between positively and negatively charged R-groups.
  • Disulfide Bridges: Strong covalent bonds formed between the sulfhydryl groups (-SH) of two cysteine amino acids.

Quaternary (4°) Structure

• Definition: The spatial arrangement of two or more polypeptide chains (subunits) to form a single functional protein complex.
• Requirement: This level of structure only exists in proteins composed of multiple subunits.
• Example: Hemoglobin is a globular protein made of four polypeptide subunits (two α-chains and two β-chains) that work together to transport oxygen.
• Bonding: Stabilized by the same types of interactions found in tertiary structure (hydrophobic, hydrogen bonds, ionic bonds, etc.) between the different subunits.

5. Nucleotides and DNA/RNA

Nucleic acids are polymers specialized for the storage, transmission, and use of genetic information.

5.1. Nucleotides

Nucleotides are the monomers of nucleic acids. Each nucleotide consists of three components:

1. A Pentose (5-Carbon) Sugar:
   • Deoxyribose in DNA (lacks an oxygen atom on the 2' carbon).
   • Ribose in RNA (has a hydroxyl group on the 2' carbon).
2. A Phosphate Group: Attached to the 5' carbon of the sugar.
3. A Nitrogenous Base: Attached to the 1' carbon of the sugar.
   • Pyrimidines (one ring): Cytosine (C), Thymine (T, only in DNA), Uracil (U, only in RNA).
   • Purines (two rings): Adenine (A), Guanine (G).

5.2. DNA (Deoxyribonucleic Acid)

• Function: The molecule of heredity. It stores the genetic instructions for the development, functioning, growth, and reproduction of all known organisms.
• Structure: The Double Helix
  • Two Polynucleotide Strands: DNA consists of two chains of nucleotides coiled around each other.
  • Sugar-Phosphate Backbone: The nucleotides are linked by phosphodiester bonds between the 3' carbon of one sugar and the 5' phosphate of the next, forming a backbone on the outside of the helix.
  • Antiparallel: The two strands run in opposite directions (one is 5'→3', the other is 3'→5').
  • Complementary Base Pairing: The strands are held together by hydrogen bonds between the bases.
    • Adenine (A) pairs with Thymine (T) via two hydrogen bonds.
    • Guanine (G) pairs with Cytosine (C) via three hydrogen bonds.

5.3. RNA (Ribonucleic Acid)

• Function: Plays a central role in converting the genetic information stored in DNA into proteins.
• Structure:
  • Sugar: Contains ribose.
  • Base: Uses Uracil (U) instead of Thymine (T). A pairs with U.
  • Strand: Usually single-stranded, though it can fold back on itself to form complex 3D structures.
• Major Types:
  • Messenger RNA (mRNA): Carries the genetic code from DNA in the nucleus to the ribosome.
  • Transfer RNA (tRNA): Carries a specific amino acid to the ribosome during protein synthesis.
  • Ribosomal RNA (rRNA): A major structural component of ribosomes.