Introduction to Chemical Modeling - A Laboratory Exercise

Matter is anything which occupies space and has mass. Solids, liquids and gases are all forms of matter found within and around living organisms. Each consists of one or more elements. Living matter is composed of basically four of the 92 natural elements. They are carbon (C), oxygen (O), hydrogen (H), and nitrogen (N). There are many other common elements found in living matter such as calcium (Ca), phosphorus (P), sulfur (S), sodium (Na), chlorine (Cl), iron( Fe), and iodine (I). Atoms are combined together by chemical bonds (covalent and ionic) to form molecules or formula units.

It is important to have a basic understanding of the structure of some of the important compounds found in living matter, because their structure determines their function. How many atoms combined together to form compounds is determined by its valence. Valence is the number of bonds from one atom of the element.

The molecular model set you will be using has different colored spheres to represent elemental atoms. Each sphere has one or more holes, which represent the common valence number for that element. In this laboratory exercise you will be modeling many of the fundamental compounds and functional groups found in living matter.

Below is a list of the representative elements and their colors found in the molecular modeling set:

Atom

Color

Atom

Color

carbon =black chlorine =green
hydrogen =white sulfur =yellow
oxygen =red phosphorus =purple
nitrogen =blue cation =gray, 1 hole, 2 hole

There are also plastic links to represent bonds. They are as follows:

medium link =gray, single covalent bond
long flexible link =gray, double/triple covalent bond
medium link =purple, single ionic bond
long flexible link =purple, double ionic bond

Constructing Models

In this part of the exercise you will be constructing models of some of the common molecular and ionic compounds; and functional groups found in living organisms.

Molecular Formulas

A molecular formula shows the exact number of atoms of each element which are joined in one molecule. Symbols are used to represent the element and the subscripted number following the symbol indicates the number of atoms. In water, H2O the H = hydrogen, and the 2 indicates that their are two atoms. The O = oxygen. Since there is no number following O it is assumed to be one atom.

Water

Construct a model of the water molecule. What is its molecular formula? _________. What atoms form water? __________________. What type of bonds are found in the molecule? __________________. Sketch the molecule in the space provided.

 

Methane

Construct a model of the methane molecule. What is its molecular formula? _________ Sketch the molecule in the space provided.

 

 

Ethanol

Construct a model of the ethanol molecule. What is its molecular formula? ____________.

 

 

 

 

Structural Formulas

It is very hard to draw three dimensional models of compounds, so plane view of the arrangement of atoms in a molecule are often used. Below is the structural formula for water.

The letters are the symbol for the element and the single lines represent a single covalent bond. If there are double covalent bonds then two lines are used, triple covalent bonds, then three lines. Using your models (and other resources) draw the structural formulas for methane and ethanol in the space provided.

Carbon dioxide

Construct a model of carbon dioxide. What is its molecular formula? ____________. What is its structural formula? ___________________. Does it contain double bonds? ____. How many? _______. Sketch the molecule in the space provided.

 

Inorganic Compounds

You have already made models of two inorganic molecules (water and carbon dioxide). Inorganic compounds do not contain carbon /hydrogen assemblages, whereas organic compounds do (i.e. methane and ethanol). In this part of the exercise you will construct models of inorganic compounds

Metal Chlorides

Construct a model of a metal chloride. In this model the gray sphere represents the cation, sodium (Na+). What is the formula for sodium chloride? ____________. Sketch the model in the space provided.

 

Construct a model of hydrogen chloride. When this compound is in an aqueous solution it dissociates (ionizes) to form hydrochloric acid. Sketch the model in the space provided.

 

 

Construct a model of sodium hydroxide, a base. When this substance is placed in an aqueous solution it dissociates into Na+ and OH-. In this model the oxygen and hydrogen are covalently bonded to form a hydroxyl radical, which acts as an anion. This hydroxyl radical bonds ionically to the sodium. Sketch the model in the space provided.

 

Biochemical Compounds

These organic compounds are found in living organisms and are important in the structural and functional aspects of life. The are:

In this section of the lab you will:

Nucleic acids are to large to construct from these kits but will be modeled in an upcoming lab (DNA).

Construct the following functional groups based on the structural formula (they are all covalently bonded):

Group

Structural formula

Model

Amino
Aldehyde
Carboxyl
Phosphate
Methyl
Alcohol
Ketone

Save the methyl, amino, and carboxyl groups to construct the next model.

Proteins

 

The amino acid alanine is an important component (monomer) of proteins. Using a carbon atom as the central atom construct a model of alanine.

Lipids

 

Fats are esters of glycerol with long chains (usually 3) of fatty acids (such as stearic acid) attached at the -OH positions. Construct the glycerol portion of a fatty acid.

Carbohydrates

Glucose is one of the simplest and most important monomers found in living organisms. It is from this molecule that most living organisms derive their energy through a process called cellular respiration. Construct the glucose molecule.

 

 

 

 

Review Questions

Define the following:

What is valence and why is it important?

Structure determines ________________________?

Draw the structural formulas for:

Sketch Page

Water

Methane

Ethanol

Carbon dioxide

Sodium chloride

Hydrogen chloride

Sodium hydroxide

   
Maintained by John M. Patterson
Assistant Professor of Biology, Paul D. Camp Community College
Pages last updated on September 9, 2009