Biomolecules and Enzyme Function: General Biology Study Notes

Polymers and Monomers

Dehydration Synthesis and Hydrolysis

Biological macromolecules are formed by linking monomers through dehydration synthesis, and broken down by hydrolysis.

• Dehydration synthesis: Removal of water to join two monomers.

• Hydrolysis: Addition of water to break a polymer into monomers.

Carbohydrates

Glucose Monomers and Structures

Carbohydrates are organic molecules composed of carbon, hydrogen, and oxygen, typically in a 1:2:1 ratio. Their structure and function depend on the type of glycosidic linkage between glucose monomers.

• Shape depends on glycosidic linkage type: The orientation of glycosidic bonds determines the structure and digestibility of polysaccharides.

• Examples and uses:

  • Glycogen: Storage form of glucose in animals.

  • Amylose: Unbranched starch in plants.

  • Amylopectin: Branched starch in plants.

  • Cellulose: Structural polysaccharide in plant cell walls.

• Uses:

  • Energy storage (glycogen, starch)

  • Structural support (cellulose)

  • Why can humans not digest cellulose? Humans lack the enzyme cellulase needed to break β(1→4) glycosidic bonds in cellulose.

Lipids

General Structure and Function

Lipids are hydrophobic molecules that serve as energy storage, structural components of membranes, and signaling molecules.

• General structure: Mostly hydrocarbons; includes fatty acids, triglycerides, phospholipids, and steroids.

• Formation: Fatty acids are linked to glycerol by ester bonds.

• Properties depend on nature of fatty acids:

  • Saturated vs. unsaturated: Saturated fats have no double bonds; unsaturated fats have one or more double bonds, affecting fluidity.

  • Cis vs. trans fats: Cis fats have hydrogen atoms on the same side of the double bond, while trans fats have them on opposite sides, impacting health.

• Phospholipids: Major component of cell membranes; form bilayers due to hydrophilic heads and hydrophobic tails.

• Micelles: Spherical lipid structures formed in water.

• Bilayers: Double-layered structures forming the basis of biological membranes.

• Cholesterol: Steroid that stabilizes membrane fluidity and serves as a precursor for steroid hormones.

Proteins

General Amino Acid Structure and Polymerization

Proteins are polymers of amino acids linked by peptide bonds. Their structure determines their function.

• General amino acid structure: Central carbon, amino group, carboxyl group, hydrogen, and variable R group.

• Polymerization: Amino acids are joined by peptide bonds through dehydration synthesis.

• Four levels of protein structure:

  • Primary: Sequence of amino acids.

  • Secondary: Local folding (α-helix, β-sheet) stabilized by hydrogen bonds.

  • Tertiary: Overall 3D shape due to interactions among R groups.

  • Quaternary: Association of multiple polypeptide chains.

• Forces that contribute to protein conformation: Hydrogen bonds, ionic bonds, hydrophobic interactions, disulfide bridges.

• Denaturation: Loss of protein structure due to heat, pH, or chemicals.

• Conditions that contribute to denaturation:

  • Aggregates and disease examples involving aggregates (e.g., Alzheimer's disease).

• Role of chaperones in protein folding: Chaperone proteins assist in proper folding and prevent aggregation.

Enzyme Structure and Function

Active Sites and Models

Enzymes are biological catalysts that speed up reactions by lowering activation energy.

• Active sites: Region where substrate binds and reaction occurs.

• Lock and key model & induced fit model:

  • Lock and key: Substrate fits exactly into the active site.

  • Induced fit: Enzyme changes shape to accommodate substrate.

• Regulation (examples):

  • Cofactors: Non-protein molecules required for enzyme activity.

  • Allosteric activators: Molecules that increase enzyme activity by binding to sites other than the active site.

  • Allosteric inhibitors: Molecules that decrease enzyme activity by binding to allosteric sites.

Reaction Coordinate Diagrams

Enzyme Effects on Activation Energy

Reaction coordinate diagrams illustrate the energy changes during a chemical reaction.

• Enzymes lower activation energy: Enzymes reduce the energy barrier for reactions.

• Enzymes don't alter ΔG: The overall free energy change ($riangle G$) of a reaction remains unchanged.

• Spontaneous vs. non-spontaneous reactions:

  • Spontaneous: $riangle G < 0$

  • Non-spontaneous: $riangle G > 0$

Linked / Coupled Reactions

ATP Hydrolysis and Cellular Power

Cells use energy from spontaneous reactions to drive non-spontaneous ones through coupling.

• Energy coupling: Energy released from ATP hydrolysis ($ATP ightarrow ADP + P_i$) is used to power cellular processes.

• Example: ATP hydrolysis drives active transport, muscle contraction, and biosynthesis.

Additional info: Coupled reactions are fundamental to metabolism, allowing cells to perform work that would otherwise be energetically unfavorable.