BIOCHEMISTRY
Biological Molecules Lab
Objective:
Learn some basic functional groups found in organic molecules
Be able to write structural formulas when given a molecular formula.
Background Information:
Biochemistry is the science that studies the chemical reactions in living organisms.
Carbon, oxygen, nitrogen and hydrogen are four elements (and sometimes nitrogen and phosphorus) that
combine in many ways to form many of the molecules of organisms. In some organisms, these elements make
up over 90% of the weight of the organisms. Other elements are present but in much smaller amounts.
Carbon is the major element that makes life possible; molecules containing carbon are organic molecules.
Molecules that do not contain carbon are called inorganic molecules.
Hydrocarbons constitute a large group of organic compounds. They contain the elements hydrogen and
carbon. Often another atom, other than carbon or hydrogen, or a group of atoms is substituted on the
hydrocarbon molecule. This substitute group of atoms is called a functional group. Functional groups are
defined as a group of atoms that give a molecule its characteristic shape.
The chemical properties of an organic molecule are determined by the functional group. For example,
C2H6 is a gas called ethane. By removing one of the hydrogen atoms and adding a hydroxyl group ( __ OH), the
substance becomes a liquid called ethyl alcohol. It can also be called ethanol. The formula for ethanol is
C2H5OH.
(Remember that the line – indicates one covalent bond)
For convenience, biochemists use the letter “R” to represent the part of a molecule other than the
functional group. The R can also be used to show the location of the functional group in a molecule. For
example, instead of writing CH3OH for methyl alcohol, you could write R—OH. This way the complete structural
formula does not have to be written.
Although you may be unfamiliar with the synthesis of organic molecules by organisms, this knowledge
will become more important to you as you continue your study of biology.
Materials
Model kits (optional)
Procedure:
With the help of the three tables, use the molecular formulas of the following compounds to write twodimensional structural formulas of each compound. You may want to use the model kits to build a 3-D model
(black = carbon, white = hydrogen, blue = oxygen, red = nitrogen).
1.
2.
3.
4.
5.
6.
7.
8.
9.
H2O
CH4
CH3OH
CH3CH2OH
CH3CHO
CH3COOH
CH3CH2COOH
CH3CH2NH2
NH2CH2COOH
water
methane
methyl alcohol
ethyl alcohol
acetaldehyde
acetic acid
propionic acid
ethylamine
glycine (amino acid)
Table 1: Number of Bonds Per Element
hydrogen (H)
oxygen (O)
nitrogen (N)
carbon (C)
1
2
3 or 4 (usually 3)
4
BIOCHEMISTRY
Table 2: Alkane Hydrocarbons
methane
ethane
propane
butane
pentane
hexane
heptane
octane
nonane
decane
Table 3: Functional Groups
FORMULA
STRUCTURAL
FORMULA
GROUP NAME
alcohol
R—OH
carboxylic acid
(organic acid)
R—COOH
amine
R—NH2
aldehyde
R—CHO
Questions:
CH4
C2H6
C3H8
C4H10
C5H12
C6H14
C7H16
C8H18
C9H20
C10H22
EXAMPLE
R—OH
Use the structural formulas you drew to answer the questions below.
1. Which of the nine molecules you built are not organic models? Explain.
2. Which element forms the “backbone” of most two-dimensional organic compounds?
3. Using your structural formulas and functional groups, complete the chart below:
Type of Molecule
Alcohol (e.g. ethyl alcohol)
Aldehyde (e.g. acetaldehyde)
Organic acid (e.g. propionic acid)
Amino acid (e.g. glycine)
Name of Functional Group
Structure of Functional Group
(Draw)
BIOCHEMISTRY
4. Glycerol has the structure:
What is an alcohol?
5. a)What part of the molecule gives acetic acid and propionic acid their acid properties?
b) What makes these acids different from each other?
6. Look at the formulas in Table 2. Explain what the following prefixes mean:
a) pentab) heptac) deca7. Ethyl alcohol’s formula can be written CH3CH2OH or C2H6O.
Dimethyl ether’s formula can also be written C 2H6O, but its structure is :
Molecules such as dimethyl ether and ethyl alcohol which have the same molecular formula (e.g. C2H6O) are
called isomers. Define isomers in your own words.