Can you attempt building models of biomolecules using commercially available atomic models (Ball and Stick models).

Gather materials

• Obtain a commercial ball-and-stick molecular model kit with color-coded atom spheres (e.g., C black/grey, O red, N blue, H white, P orange, S yellow) and bond connectors of varying lengths and flexibilities

• Secure reference structural formulas or 3D coordinates (textbook diagrams, Protein Data Bank files, or chemical drawing software prints)

Select target biomolecule

• Choose based on educational goals (amino acids, monosaccharides, nucleotides, small peptides)

• Limit initial builds to molecules under ~20 heavy atoms for manageable assembly

Review bonding and geometry rules

• Identify each atom’s hybridization: sp³ tetrahedral (109.5°), sp² trigonal planar (120°), sp linear (180°)

• Note functional group geometry: carboxyl C=O, amino pyramidal N, phosphate tetrahedral P

Plan the assembly sequence

• Sketch the backbone first (e.g., glycerol backbone for lipids, sugar ring for carbohydrates, peptide backbone for proteins)

• Number atoms in your reference and map to the kit’s spheres

Assemble backbone atoms

• Connect central atoms using single-bond connectors, maintaining approximate bond lengths by choosing the correct connector length

• Use rigid connectors for double bonds if kit supplies them to fix planar geometry

Add side chains and functional groups

• Attach remaining atoms in order, observing angle guides on connectors or kit instructions

• For rings (e.g., glucose), assemble sequentially and snap ends together last to close the ring

Verify stereochemistry

• Check chiral centers by comparing your model to Fischer or Haworth projections

• Swap substituents on any incorrect stereocenters before finalizing

Refine and secure the model

• Ensure all connectors are fully seated and angles match known bond angles within kit tolerances

• Replace any flexible connectors with rigid ones for teaching static conformations

Label and document

• Use small adhesive labels or colored tape to mark atom numbers or functional groups

• Photograph multiple views and annotate key features (e.g., hydrogen-bond donors/acceptors, reactive sites)

Examples of initial builds

• Glycine: build NH₂–CH₂–COOH backbone, illustrate amine and carboxyl geometries

• α-D-Glucose: assemble six-membered ring, emphasize chair conformation and hydroxyl orientations

• Adenine nucleotide: construct adenine base, ribose sugar, and phosphate linkage

Teaching and presentation tips

• Use models to demonstrate conformational changes (rotate around single bonds)

• Compare models of saturated vs. unsaturated fatty acids to show kinked chains

• Group student teams to build macromolecular fragments and assemble larger complexes collaboratively