Pattern Matching: Classifying Organic Molecules

Adapted from Kim Foglia, Explore Biology…at least as far as I can tell

Background: You have previously learned about the four classes of

large biological molecules: lipids, nucleic acids, proteins, and
carbohydrates. In this activity, you will work with a group to identify
the major classes of organic molecules and distinguish the features of
each class of molecules. There may be as many as 10,000 different
kinds of molecules in a living thing. (There will be an optional
discussion thread if you want to talk through some of this with others.)

In this activity you will examine, distinguish the features of, and
classify 45 different molecules.
 Which elements are present in each type of molecule?
Start by filling in the table, writing “Always,” “Sometimes,” or “Never” in each box.

Carbon Hydrogen Nitrogen Oxygen Phosphorus Sulfur

Always Always Sometimes

Proteins Always Always
Sometimes

Always
Carbohydrates Always sometimes Always sometimes sometimes

Nucleic Acids Always Always Always Always Always Never

Always
Lipids Always Sometimes Always Sometimes Sometimes
Sorting Slides
On the next seven slides, you’ll find
moveable cards with the molecular
structure of a macromolecule. Drag
and drop each card into the correct
category.

If you are unsure, leave the card at

the bottom of the slide as an
“Unknown.” You’ll have a chance
later to go back and determine the
correct category for that molecule.
Proteins Carbohydrates Nucleic Acids Lipids
Proteins Carbohydrates Nucleic Acids Lipids
Proteins Carbohydrates Nucleic Acids Lipids
Proteins Carbohydrates Nucleic Acids Lipids
Proteins Carbohydrates Nucleic Acids Lipids
Proteins Carbohydrates Nucleic Acids Lipids
Proteins Carbohydrates Nucleic Acids Lipids
 Once all the cards have been sorted, describe the patterns, shapes, and/or
functional groups you noticed that led you to sort the cards as you did.

Things We Noticed…
When there was a plus shape with the single and double bond one one side creating a
Proteins
V-shape

Carbohydrates

Nucleic Acids The nucleic acids had three

Lipids tended to be long chains with a single and a double bond at the end creating a
Lipids V-shape, or with rings
PROTEINS
Proteins are molecules that play many important roles in the body, including muscle structure, hormones,
antibodies to neutralize pathogens, hemoglobin for carrying oxygen, transport proteins for moving
molecules across cell membranes, chemical messengers in the nervous system, and many, many more.
What is the monomer of a protein called? Answer: amino acids

Figure 1 shows a “generic” amino acid, or one that doesn’t have a side chain, or “R group.” Two amino
acids are joined by dehydration synthesis reactions to form a dipeptide; when three or more amino acids
are joined, they are referred to as a polypeptide. Once a polypeptide has folded into a functional
conformation (shape) it is referred to as a protein. When amino acids are joined together, the “-N-C-C-“ in
the center of the molecule is known as its backbone and is a defining feature of amino acids. A typical
protein chain may contain 150 – 1000 or more amino acids. There are 20 common amino acids that are
used to build protein molecules. Cells string amino acids together end-to-end as shown in Figure 2.
 PROTEINS

Each amino acid has a different side group that is represented by “R”
in Figures 1 and 2. Two amino acids with their particular side groups
are shown in Figure 3.

Focusing only on the cards you placed in “Proteins,” copy and paste all the amino acids onto the next slide. When copying
from a slide, hold the “shift” button to select multiple cards, select “Copy”, then click back to the slide and “Paste”

How many did you originally identify? You should have 14. If you don’t have all 14 amino acids, sort through your other
piles, beginning with “Unknown” until you find all 14 amino acids. List the cards numbers here of your amino acids:
6, 5, 13, 9, 16, 15, 18, 21, 26, 27, 28, 24, 25, 20,
Proteins – Copy and paste all the cards identified as proteins
Sort the cards so you can see the card numbers.
 PROTEINS

We will now look more closely at these 14 amino acids. Bearing in mind
that the properties of the R-group determine the behavior of the amino
acid, separate the amino acids into two categories: polar and non-polar.

Hint: A highly electronegative atom on the end of an R-group will cause

the amino acid to be polar and a series of hydrocarbons on the end of an
R-group will cause the amino acid to be nonpolar.

GO ON TO NEXT SLIDE FOR SORTING 🡪

 Proteins – Using the “shift” button, select the 14 cards from the slide with the amino acid
cards, then paste again here. Sort the cards into polar and non-polar groupings.

POLAR NON-POLAR
 Proteins – Copy and paste all the cards identified as proteins
You should find 6 non-polar amino acids and 8 polar amino acid cards.
List the cards by number in this chart:
Which type of amino acids (P/NP) are more likely to be
Polar Non-Polar found on the interior of a globular protein that exists in
20 27
the cytosol of the cell?
25 13
P
9 26
28 24
Looking even more closely at the polar amino acids, you
15 2
should find three that have a charged R-group. List the cards
18 16
here of the charged amino acids:
5
21 15, 18, ?

Last, find the ONE amino acid that has a terminal (end)
sulfur atom that could engage in a “di-sulfide bridge.”
What’s its card number?

26
 Carbohydrates
Carbohydrates are also versatile molecules that store energy and provide structure to organisms. You may have
heard of simple carbohydrates, sugar, or complex carbohydrates, such a fiber. Sugars occur as ring structures.

There are monosaccharides (single rings), disaccharides (double rings), and larger structures called polysaccharides.
In solution, single rings can dynamically change from straight chains to rings and back to straight chains. A straight
chain sugar is shown below. Notice that every carbon has an oxygen atom attached to it.

Sugars can be joined together in long chains to form

macromolecules called starch, cellulose, and glycogen. A
plant’s starch and an animal’s glycogen are easily broken
down into sugars for energy. Cellulose, on the other hand,
which is made primarily in plants, can be broken down only
by a few organisms in the world – primarily the bacteria in
the guts of termites. Yet all three types of macromolecules
are made of long chains of monosaccharides, and cellulose
differs only by a small change in the connecting bond
between each pair of sugars.
Copy and paste all carbohydrate cards. You should have 11 of them. If you don’t, sort through your pile of unknowns to search
for more. Remember, carbohydrates only contain carbon, oxygen, and hydrogen in a very specific
1 carbon: 2 hydrogen : 1 oxygen ratio.

(List the cards numbers here of your carbohydrates)

Using the shift button, select all the carbohydrate carbs from the previous slide and copy and paste here. You will sort them by
type: monosaccharides, disaccharides, and polysaccharides.

Monosaccharides Disaccharides Polysaccharides

 CARBOHYDRATES
Refer to the previous slide to answer these questions:

Which cards are straight chain monosaccharides? 36, 22, 1 , 12 , 34

Which cards are ring monosaccharides? 29 & 3

Which cards are disaccharides? Which card is a polysaccharide?

10 & 40 23

Look again at your two disaccharides. One of them is common table sugar. Look
up “sucrose” in your book or online. Which two monosaccharides combine to
form sucrose? Which atoms are removed during the bonding of the two
monosaccharides?
A molecule of glucose and one of fructose combine to form sucrose. One oxygen atom and two
hydrogen atoms are removed.
 Lipids
Lipids are a diverse group of molecules that share one important trait: they are hydrophobic.
Lipids are most easily recognized by having lots of hydrocarbons, which contain non-polar
covalent bonds. Lipids may have a few polar bonds associated with oxygen, depending on the
specific molecule, but on the whole lipids consist mostly of hydrocarbons.

Lipids vary widely in both form and function and include things like waxes and pigments. In
this activity we’ll focus on fats, phospholipids, and steroids.

First, ensure you have all of the lipid cards – there are 8 of them. Look for molecules that
have long chains or rings of hydrocarbons.
Lipids – copy and paste the 8 lipid cards here.
 Lipids
Steroids are one type of molecule in the class of compounds
known as lipids. Cholesterol, shown at the right, is a steroid,
and plays an important role in membrane formation. Steroids
can be recognized by their multiple rings of carbon atoms
connected together.

Find the 3 steroids in your lipid cards. Copy and paste them
here:
 Lipids
It’s useful to keep in mind that, like proteins, molecules can have regions that are nonpolar and
regions that are polar. This is incredibly important in cell membrane functions. Re-examine the
cholesterol molecule. Use the “Insert” shape tool to put a circle on the region of the molecule
that is polar.
 Lipids
Fats and Fatty Acids
Among your cards you should have some long hydrocarbon chains with a
carboxyl group at one end. One of the defining features of these
hydrocarbon chains is the absence of oxygen except in one carboxyl group at
one end of the molecule.
O
||
Type/draw a carboxyl group here: O-C

Is a carboxyl group polar or non-polar? The presence of which element tells

you this?
Polar; Oxygen
 Lipids
Fatty acids can exist alone as a single chain of hydrocarbons or can join a glycerol molecule to form
larger molecules with multiple chains. The chains themselves can vary in terms of the presence or
absence of double bonds between the carbon molecules.
Fatty acids that contain no double bonds are considered saturated.
Fatty acids that contain at least one double bond are considered unsaturated.
Saturated fats are solid at room temperature because the chains pack together more densely than
do unsaturated fats, which are liquid at room temperature and less dense. Saturated fats tend to
be found in land animals; unsaturated fats tend to be found in plants and fish.

Copy and paste the three cards that show individual fatty acid chains.
Look more closely at these three cards. Which
chains are saturated? How can you tell?

None are saturated because they all have a

double bond

Which chain is unsaturated? How can you tell?

They are all unsaturated because they all have a
double bond
 Lipids
Fats, as you consume them in your food, are formed by joining three
fatty acids to a glycerol molecule. In addition to the number of
double bonds, the length of the fatty acid chains can also vary.
Which card shows a molecule that is a fat?

This fat is known as a

triacylglycerol, or a triglyceride.
(Copy and paste the card with the fat molecule and place here)
This is one of the molecules that is
found in your blood. Doctors track
the amount of triglycerides found
in blood. Too much triglyceride in
your blood is a possible indicator of
heart disease.
 Lipids
The last remaining lipid is a phospholipid. Look closely to see that there are two fatty acid
chains attached to a glycerol. The third carbon on the glycerol molecule has a phosphate
attached to it.
Which card is the phospholipid?
Is a phosphate group polar or nonpolar? (Copy and paste the card with the phospholipid molecule and
place here)
POLAR
Are the fatty acid chains polar or nonpolar?
POLAR Phospholipids are essential for cells because they are
major constituents of cell membranes. In this diagram
This molecule is “amphipathic,” meaning that of a cross-section of a cell membrane, insert a rectangle
is has both hydrophilic and hydrophobic around the nonpolar and circles around the two regions
regions. On this simplified diagram of a that are polar.
phospholipid, insert a circle around the polar
region and a rectangle around the nonpolar
region of the molecule.
Nucleic Acids - Nucleic Acids store, transmit, and help express hereditary information. You should have 12 cards
remaining. Copy and paste them here:

(List the cards numbers here of your nucleic acids)

 Nucleic Acids
The monomer of nucleic acids are nucleotides, which themselves contain a nitrogenous
base, a sugar, and anywhere from 1 to 3 phosphate groups. Five of your cards contain only
the nitrogenous bases: a single or double-ring structure that contains nitrogen. Identify the
five nitrogenous bases. Ensure the cards you select do not contain a pentose sugars, as
shown here:

(Paste the five cards that contain only the nitrogenous bases here)
 Nucleic Acids
Nitrogenous bases are either pyrimidines (single ring structures) or purines
(double ring structures). Which of the five cards are pyrimidines?
(Identify by number): 8 & 19

Which of the five cards are purines? 4,7 & 30

The nitrogenous base connects directly to a pentose sugar, either

ribose in RNA or deoxyribose in DNA. In the diagram above, circle
the Oxygen that is present on ribose that is absent on deoxyribose. 41, 19, 45, 43
You have four cards that show a nitrogenous base attached to a
pentose sugar. When molecules are in this state, they care called
nucleosides. Which cards are these?
Look closely at the sugars on each card. Do
these molecules contain ribose or deoxyribose?
deoxyribose
 Nucleic Acids
When nucleosides combine with one, two, or three phosphates they are then nucleotides.
The more phosphates that are present, the more energy contained in the molecule.
Adenosine triphosphate (ATP) is not only a major subunit of DNA and RNA, but also a major
energy carrier in living systems. How many phosphate groups should you expect to find in
adenosine triphosphate?
3

Which of your cards contains ATP?

32

When ATP is used for cellular energy, water hydrolyzes the terminal phosphate group from
the ATP, leaving only two phosphates behind – a molecule called adenosine diphosphate.
Which of your cards contains ADP?
30 & 31
 Nucleic Acids
Through a process called cellular respiration, glucose is broken down and the
terminal phosphates that were removed are added back on to ADP, so these
molecules are continuously recycled by the cell. While nucleotides that are
free floating in the cell’s cytoplasm typically consist of three phosphate
groups, when each is added to a growing molecule of DNA or RNA, the end A nucleotide
two phosphate groups are removed by dehydration synthesis, leaving only
one phosphate group. Which of your cards contains a molecule that looks like
this?
On the molecule of a different nucleotide to Nitrogenous
Base
the right, label the phosphate, pentose, and
Phosphate
nitrogenous base. The single pentose sugar
and the single phosphate group on each
nucleotide join with others to form a
sugar-phosphate backbone of a molecule,
with the nitrogenous bases on the interior of
the molecule. Pentose
 Nucleic Acids
Now examine this molecule:

Which letter represents the phosphate group?

Z

Which letter represents the pentose sugar?

Y

Which letter represents a purine?

W

Which letter represents a pyrimidine?

X