MANILA ADVENTIST COLLEGE

1975 Donada St. Pasay City

Name: __________________________________ Date: ____________________

Course, Year and Section: __________________ Grade: ___________________

BIOCHEMISTRY LAB ACTIVITY NO. 3

Constructing 3-D Models of Some Common Biomolecules

INTRODUCTION

3-D models of molecules are important to visualize how they look like, to identify different groups
present in the molecule and how they are oriented, and to understand how the molecule behave in a
three dimensional environment.

In this dry lab, students will construct 3-D models using materials that are readily available in the
community.

NEEDED MATERIALS (PER INDIVIDUAL BASIS)

1 kg Calamansi fruits
1 box toothpick
1 box thumbtacks
Red crayon
1 pc clean paper
Cellphone (for picture taking and documentation)

PROCEDURE

1. Draw the chemical structure of the molecule under study and show all its lone pairs.
 Thankfully, the chemical structures of some common biomolecules are already given
below.
2. Draw all the lone pairs in the structure.
 A lone pair is a pair of valence electrons that is not used for bonding.
 To determine how many lone pairs an atom has, recall the number of valence electrons
of that atom, then assign one valence electron to each of its hands. Place any excess
valence electrons anywhere around the atom, then encircle each pair of excess
electrons to represent a lone pair.

TABLE 1
Element C H O N N P P S S Halogen family
# valence 4 1 6 5 5 5 5 6 6 7
electrons
# “hands” 4 1 2 3 5 3 5 2 6 1
# of lone 0 0 2 1 0 1 0 2 0 3
pairs
Note: Nitrogen (N) and phosphorus (P), usually use 3 “hands” but sometimes, they use 5 “hands”.
Similarly, sulphur (S) usually uses 2 “hands” but sometimes, it uses 6 “hands” in the structure.

3. Encircle all the central atoms of the chemical structure and determine their respective
geometric shape.
 A central atom is an atom with 2 or more attached groups
 The geometric shape of a central atom is based on its number of attached groups and its
number of lone pairs.
 Use the table given below to determine the geometric shape of a central atom given its
number of attached groups and number of lone pairs

TABLE 2
Electron domain # attached groups # lone pairs Geometric shape Angle/s
2 2 0 Linear 180
degrees
3 3 0 Triangular planar 120˚
2 1 Bent 120˚
4 4 0 Tetrahedral 109.5˚
3 1 Pyramidal 109.5˚
2 2 Bent 109.5˚
5 5 0 Trigonal 120˚, 90˚
bipyramidal
4 1 Seesaw 120˚, 90˚
3 2 T-shape 90˚
6 6 0 Octahedral All 90˚
5 1 Square pyramid 90˚
4 2 Square planar 90˚
3 3 T-shape 90˚

4. Using calamansi fruits to represent atoms, toothpicks to represent chemical bonds, and thumb
tacks to represent lone pairs, construct a 3-D model of the structure of the molecule under
study based on the respective geometric shapes of its central atoms.
 Your lab instructor will demonstrate to you how it is done, or
 You may watch the tutorial video on constructing 3-D model of molecules posted in our
ms teams for biochem lab

5. Colour all toothpicks that represent polar covalent bonds using red color.
 Polar covalent bond is the chemical bond formed between two non-identical non-metal
atoms

6. When you’re done with the 3-D model, take a picture of it, print the picture and paste it on a
clean bond paper.
7. Finally, keep the finished product for future reference
8. Repeat procedures 1 to 6 for the next molecule.
BIOMOLECULES: Alanine, Propionic Acid, Glucose, Dopamine

Alanine, an amino acid Propionic acid, a fatty acid Glucose, a monosaccharide

Glycerol, an alcohol dopamine, a neurotransmitter

DATA

Number of central Number of lone pairs Number of polar

atoms covalent bonds
Alanine
Propionic acid
Glycerol
Glucose
Dopamine

QUESTIONS

1. What is an amino acid?

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2. What are the roles of amino acids in the body?
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3. What is a monosaccharide?
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4. What is the role of glucose in our body?
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5. What are fatty acids, and what are their roles in our body?
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6. What biomolecule is formed when a glycerol reacts with 3 fatty acids?
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7. What is a neurotransmitter?
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8. What is the significance of dopamine as neurotransmitter?
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9. Based on their respective structures, can you say that all of the biomolecules given above are
organic compounds? Why or why not?
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