Notes on Biology

My main question is - how can we grow trees faster? How can we grow trees using electricity, instead of photosynthesis? These are guiding my research into how organisms are built, how they work, how does DNA work, etcetera.

Reading:

• Molecular Biology of the Cell
• Resources for learning bioinformatics
• geohot reverse-engineering corona

Hierarchy of an organism.

From low-level to high-level.

• Atoms
• Molecules - bonded atoms
  • Arginine - type of complex molecule
  • Some molecules are small (water, glucose), others large (DNA, proteins).
    • The biggest is titin (titan)
  • Types:
    • Amino acid
      • Types of molecules containing:
        • amine group (–NH₂)
        • carboxyl group (–COOH)
        • side chain
• Polymers - chains of molecules
  • Protein
    • Chain of molecules (amino acids), linked via peptide bond
      • Amino acid + amino acid → peptide bond + water
  • DNA
    • Chain of molecules (nucleotides)
    • The information is in the order of the nitrogenous bases (A, T, C, G) along the DNA strand
      • The backbone (sugar-phosphate) just holds the chain together—it doesn’t store information.
  • Genes
    • A specific sequence of positions in DNA
    • e.g. type 1 diabetes HLA-DR3
      • composed of the HLA-DR17 and HLA-DR18 split ‘antigens’ serotypes
        • HLA-DR
          • human leukocyte antigen (HLA) system is a complex of genes on chromosome 6
            • Chromosome
              • DNA → double helix → wraps + folds → chromosome.
              • Each chromosome = one very long DNA molecule + proteins
              • DNA = chains of molecules (nucleotides).
              • Chromosome = one long DNA chain, folded + packaged with proteins.
              • Pairs of chromosomes = two similar chromosomes (one from each parent).
              • Genome = 46 chromosomes (23 pairs). One set from dad, one set from mum.
• Cells
  • Collections of molecules and polymers
  • Minimum viable cell:
    • Lipids + nucleic acids + proteins + small molecules.
      • Membrane → made of lipid molecules (to keep inside/outside separate)
      • Genetic material → DNA (or RNA in some viruses)
      • Ribosomes → made of RNA + protein (to build proteins)
      • Enzymes → proteins (to catalyze reactions)
      • Energy molecules → like ATP
      • Basic nutrients → sugars, amino acids, ions (as raw materials)
• Tissues
  • Groups of similar cells working together.
  • Example: xylem (wood), epidermis (skin), mesophyll (leaf interior).
• Organs
  • Multiple tissues combined into a larger structure with a specific function.
  • Example: leaf, root, stem, flower.
• Organ systems
  • Coordinated groups of organs.
  • Example: shoot system (stems + leaves), root system.
• Whole organism
  • Basil plant

How does cell growth and DNA work?

Single-celled organism (core loop)

1. Cell contains DNA (code archive)

• Physical reality: a long molecular string sitting in the nucleus (or cytoplasm if prokaryote).
• Function: holds instructions (genes) and control tags (regulatory regions).

2. Proteins inside the cell read which DNA segments are needed (pointer lookup)

• Physical: pre-existing proteins (from parent cell or previous state) physically bind to DNA at specific spots.
• Function: select which instructions to copy.

3. Copy DNA instruction into a working script (mRNA)

• Physical: RNA polymerase enzyme moves along DNA, copying the gene sequence into a smaller, mobile molecule (mRNA).
• Function: create a temporary, portable version of the instruction.

4. Compile working script into new proteins (functional parts)

• Physical: ribosomes attach to mRNA and assemble a chain of amino acids → folds into a protein.
• Function: build machines that carry out new tasks (growth, division, sensing, movement).

5. Proteins change the cell’s state (growth, division, response)

• Physical: proteins catalyze reactions, create structures, or change other proteins.
• Function: cause physical growth (more mass), replicate DNA, divide the cell, or respond to signals.

Repeat

• Newly made proteins feed back to influence which genes get read next → the cycle continues.