Cell Chemistry and Biosynthesis

Cell Chemistry and Biosynthesis

Overview

• Course: Bio 209

• Source: Hillis, DM. Principles of Life, 2nd Edition. WH Freeman.

Major Themes of Cellular Metabolism

Chaleteral Synthesis

• Involves bonds and the connection between structures.

Glycogen and Galactose Metabolism

• Key pathways for energy storage and utilization.

Steroid Hormone Synthesis

• Important for signaling and regulatory functions in the body.

Complete Map of Metabolic Pathways

• Includes contributions from various biological molecules:

  • Carbohydrates

  • Amino acids

  • Nucleotides

  • Lipids

  • Ketone bodies

Learning Objectives for The Week

• Identify biomolecules based on chemical structure and characteristics.

• Recognize important chemical groups in biomolecules.

• Understand general mechanisms of enzyme action.

Levels of Biological Organization

Hierarchy of Biological Structures

1. Molecular level:

   • Atoms (Carbon, Hydrogen, Oxygen, etc.)

   • Small molecules (e.g., water, methane)

   • Large biomolecules (proteins, nucleic acids)

2. Cellular level:

   • Cells and their functions

   • Specialization of cells into tissues

3. Organ system level:

   • Organs and organ systems in multicellular organisms

   • Interactions in ecosystems including biosphere interactions

Miller & Urey Experiment

Methodology

• Input: Simple chemicals (H₂O, N₂, NH₃, H₂)

• Process: Heat applied, electrical sparks simulate lightning to create conditions for synthesis.

• Result: New organic compounds formed, including purines, pyrimidines, and amino acids, collected in a condensed liquid.

Conclusions

• Demonstrates the potential for abiotic synthesis of organic compounds, illustrating early Earth conditions and biochemical evolution.

Cellular Composition

Macromolecules in Cells

• Every living organism maintains similar proportions of four macromolecules:

  • Proteins

  • Nucleic acids

  • Carbohydrates (polysaccharides)

  • Lipids

  • Approximately 70% water by weight.

Macromolecule Formation Processes

1. Condensation Reaction

   • Involves removing water to form covalent bonds between monomers (e.g., nucleotides forming nucleic acids).

   • Reaction:
     $ext{Monomer}<em>1 (H ext{-}) + ext{Monomer}</em>2 (OH) <br>ightarrow ext{Polymer} + H₂O$

2. Hydrolysis

   • Addition of water breaks covalent bonds between monomers.

   • Reaction:
     $ext{Polymer} + H₂O <br>ightarrow ext{Monomer}<em>1 + ext{Monomer}</em>2$

Thermodynamics in Cellular Reactions

1. First Law of Thermodynamics

   • Energy conservation: Total energy in a closed system remains constant.

   • Formula:
     $E<em>{ ext{before}} = E</em>{ ext{after}}$

2. Second Law of Thermodynamics

   • Energy transformations increase entropy; usable energy decreases over time.

   • Free energy: Amount of energy available to do work decreases after transformations.

Free Energy and Reactions

• Endergonic Reactions: Require energy input to form products at a higher energy level. Example: Active transport, synthesis reactions.

  • Energy diagram:
    $ext{Reactants} + ext{Energy} <br>ightarrow ext{Higher Energy Products}$

• Exergonic Reactions: Release energy, forming products at a lower energy level. Example: Cellular respiration, hydrolysis of ATP.

  • Energy diagram:
    $ext{Reactants} <br>ightarrow ext{Lower Energy Products} + ext{Energy}$

Metabolism and Biomolecule Categories

Carbohydrates

1. Classification and Structure

   • Cyclic structures of sugar monomers: Pentoses and hexoses.

2. Linkage Formation

   • Glycosidic bonds created through dehydration reactions in polysaccharides.

Nucleic Acids

1. Structure

   • Nucleotides composed of phosphate, sugar, and nitrogenous bases (purines and pyrimidines).

2. Phosphodiester Bonds

   • Link between nucleotide monomers forming polynucleotide chains.

Lipids

1. Types and Properties

   • Fatty acids: Saturated and unsaturated forms (kinks inhibit close packing).

   • Triglycerides and phospholipids as major components in cell membranes.

Proteins

1. Formation

   • Amino acids linked by peptide bonds: Reaction between amino group and carboxyl group.

   • Diversity from R-groups: Unique functional properties based on side chains.

2. Structures

   • Primary: Sequence of amino acids.

   • Secondary: Emergence of α-helices and β-pleated sheets via hydrogen bonding.

   • Tertiary: Overall 3D shape from folding multiple secondary structures.

   • Quaternary: Assembly of multiple polypeptides to form functional proteins.

Enzyme Function and Regulation

Role of Enzymes

• Biological catalysts that lower activation energy, increasing reaction rates without being consumed.

• Specificity for substrates due to unique active sites.

Factors Influencing Enzyme Activity

1. Concentration of substrates

   • Low concentration increases rate; saturating concentrations lead to maximum velocity (Vmax).

2. Temperature and pH

   • Each enzyme has an optimal temperature and pH for maximal activity.

3. Inhibition Mechanisms

   • Competitive Inhibition: Inhibitor competes with substrate for active site.

   • Noncompetitive Inhibition: Inhibitor binds to allosteric site, altering enzyme function.

Examples of Enzyme Action

• Aspirin as a competitive inhibitor for cyclooxygenase, modifying active site and diminishing pain mediator synthesis.

Conclusion:

• Overall integration of metabolic pathways and roles of various biomolecules is essential for the function and maintenance of life. Understanding these interactions helps in exploring biochemical processes and therapeutic approaches.