Molecules of Life 1.1

The Molecules of Life

Overview of Small Molecules

  • Importance: While large polymers (macromolecules) dominate molecular and cellular biology, small molecules are foundational as the environment for cellular processes.

  • Composition: Small molecules, including water, inorganic ions, and various organic molecules, constitute 75-80% of living matter by weight. Water alone makes up approximately 75% of a cell's volume.

  • Functions: These substances serve as substrates in numerous chemical reactions within cells, including:

    • Energy metabolism

    • Cell signaling

Acquisition of Small Molecules

  • Sources:

    • Importation: Some small molecules, such as ions and water, are taken up by cells.

    • Synthesis: Other small molecules are synthesized inside the cell through a series of chemical reactions.

Stereoisomerism and Molecular Evolution

  • Amino Acids:

    • Only L-forms of amino acids (e.g., L-serine) are incorporated into proteins; D-mirror images are not used.

    • All amino acids except glycine exhibit chirality due to an asymmetric carbon atom.

  • Glucose:

    • Only D-glucose is metabolized by cells; L-glucose is absent in nature.

  • Evolutionary Insight: Early cellular ancestors developed mechanisms that preferentially utilize one stereoisomer, locking these evolutionary choices into place.

Adenosine Triphosphate (ATP)

  • Energy Storage: ATP is a universally conserved small molecule that stores chemical energy in two of its high-energy bonds.

  • Energy Release: When ATP loses a phosphate group to form adenosine diphosphate (ADP) and inorganic phosphate (), it releases energy usable for various cellular processes:

    1. Protein Biosynthesis

    2. Muscle Contraction

    3. Cellular Movements (crawling movement, chromosome movement)

    4. Transport against Concentration Gradients

    5. Electric Potential Generation (nerve function)

    6. Heat Production

Energy Generation and Metabolism

  • Breaking Down Food: Energy is harvested from food molecules (e.g., sugars) and converted into ATP.

  • Photosynthesis: Plants and some organisms create ATP through photosynthesis, capturing sunlight energy.

  • Alternative Pathways: Some prokaryotes in extreme environments generate ATP via reactions with reduced compounds like hydrogen sulfide.

Cellular Macromolecules

  • Polymers Formation: Small molecular monomers join to form polymers (macromolecules) through a single type of covalent linkage reaction.

  • Examples:

    • Sugars: Monomers for polysaccharides like cellulose (plant cell walls) and glycogen (glucose storage in liver and muscle).

Proteins

  • Structure and Function: Proteins are the most abundant macromolecules and perform diverse cellular tasks.

    • Formed from 20 different amino acids in chains ranging from 100 to 1000 residues.

    • Folding and Shape: Proteins fold into complex three-dimensional structures essential for their function.

  • Sources of Amino Acids: Humans synthesize amino acids or obtain them through dietary proteins.

Functions of Proteins

  • Enzymatic Activity: Catalyze chemical reactions involving small molecules/macromolecules.

  • Structural Components: Form cellular structures, including the cytoskeleton for cell shape and internal transport.

  • Regulatory Roles:

    • Hormones (e.g., insulin) and receptors controlling metabolic processes and gene expression.

Nucleic Acids

  • DNA Structure: Deoxyribonucleic acid (DNA) is composed of two helical strands forming a double helix.

    • Discovery by Watson and Crick in 1953.

    • Bases: A, T, C, G with complementary pairing (A-T, C-G).

  • Functions:

    • Carries genetic information represented as the sequence of nucleotides.

    • Genes encode proteins and regulate cell function.

  • Genome Sizes: Overview of genome sizes across organisms:

    • Eubacteria (e.g., E. coli): 4.64 million base pairs, around 4,100 genes.

    • Humans: Approximately 3.3 billion base pairs, 20,800 protein-coding genes.

Gene Expression: Transcription and Translation

  • Transcription:

    • Process of copying DNA into mRNA using RNA polymerase.

    • RNA processing in eukaryotes involves splicing introns to produce mature mRNA.

  • Translation:

    • Ribosomes synthesize proteins by linking amino acids in the order specified by the mRNA.

The Role of RNA

  • Beyond Coding: RNA serves essential roles beyond protein coding, including ribozymes catalyzing chemical reactions.

  • RNA World Hypothesis: Suggests early life forms were based on RNA before evolving into DNA-protein systems.

Regulation of Gene Expression

  • Cell Type Specificity: Different cell types express unique sets of genes based on regulatory regions and transcription factors.

    • Example: Liver and muscle cells express different proteins despite having the same DNA.

Phospholipids and Membrane Structure

  • Membrane Composition: Cell membranes consist mainly of a bilayer of phospholipids with hydrophilic heads and hydrophobic tails.

  • Membrane Function:

    • Impermeable to hydrophilic compounds (e.g., water, ions) except through specific transport proteins.

    • Structural integrity supports cell shape and adhesion.

Quality Control in Cellular Macromolecules

  • Damage Repair: Cells expend energy to repair or degrade damaged macromolecules, particularly DNA.

  • Protein Misfolding: Misfolded proteins can lead to cellular damage and diseases, e.g., Alzheimer's due to aggregated proteins.

  • Mutations: Changes to DNA can cause errors in protein synthesis, leading to cell malfunction or diseases like cancer.