Zero to Genetic Engineering Hero - Chapter 3 - Growing E. coli Cells 76
Proteins are both the ‘machinery’ and ‘scaffolding’
(structure) of cells. Proteins help cause chemical reac-
tions to happen through enzymatic reactions (Chapter
6). Some proteins read DNA (Chapter 4), while others
copy and create DNA. Proteins are even essential for
creating other proteins (Chapter 5). Proteins break
molecules and other proteins apart, combine mole-
cules and reshape molecules. For example, protein
enzymes are why a lipid and a protein combined to
form peptidoglycan in the intermembrane space.
They also caused the sugar and lipid of LPS to become
connected and bind into the outer membrane.
Proteins are also an essential part of the structure
and function of cells. Like central beams that support
the factory roof, strings of proteins can form the
scaffolding of cells to help give cells structure and
shape. As we saw during our tour, proteins can be the
‘doors’ and ‘passageways’ through the inner and outer
membranes (Figure 3-24).
Proteins do a lot, but what are they and what are they
made of? Just as DNA is a string of smaller “building
block” molecules called nucleotides, proteins are a
string of smaller molecules called amino acids (Figure
3-26).
While the nucleotides that make up DNA are made
of CHOPN, amino acids are made up of CHONS, and
amino acids string together to make proteins. Proteins
do not form a double helix, that is a special character-
istic of DNA. Instead, they form a single long string of
amino acids that can fold into a three-dimensional
shape like when your headphone wire tangles up on
itself!
Comparing again to DNA, at the molecular level, the
string of nucleotides is joined together because of a
sugar-phosphate backbone (Figure 1-17). Each nucle-
otide has its own phosphate and deoxyribose sugar,
however, when combined with other nucleotides
to form a string, you see that the sugar-phosphates
are attached to other sugar phosphates to create the
backbone of DNA. The backbone of an amino acid’s
string follows the same principle, but the chemical
groups are different. Amino acids are made of three
different chemical groups - an amine (NH
2
group), a
carboxyl (COO- group) and a unique group called a
“side-group” (Figure 3-27).
Scientists call a nitrogen that is bound to two hydro-
gens (NH
2
) an “amine.” When a carbon (C) is bound to
an oxygen (O) and another oxygen with an hydrogen
(OH), it is called a carboxyl group, short for carbox-
ylic acid. As the amino acid string is created the
amine-carboxyls are slightly altered so that at the
very beginning of the string there is an amine, then
there is a repeating nitrogen-carbon-carbon (N-C-C)
backbone, and at the end is a carboxyl (Figure 3-26).
A short string of amino acids is called a peptide. When
the chains include more than ~20 amino acids, they
are called proteins. The chemical structures of all
of the different common amino acids can be found
in Figure 3-30, and these amino acids can be strung
together in any order!
Figure 3-26. Four amino acids linked together to form a chain
called a peptide. A long peptide of 20 amino acids or more is
a protein. “R” represents the variable side-group of the amino
acid that you can see more of in Figure 3-30.
N C
H
C N C
C
N C
C
N C
C
H
O
O-
Amine Carboxyl
R R R R
1 2 3 4
Anatomy of a Amino Acid
G
Glycine
Full amino acid name
The Building Blocks of Proteins
3 letter abbreviation
Single letter abbreviation
Carboxylic
Group
Side Group
Amine
Group
N
H
R
C
O
H
C
H O-
Figure 3-27. The building blocks of proteins, amino acids,
have important characteristics. An amine group, a carboxyl-
ate group and a special group that makes them unique, the
‘side-group’.
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Zero to Genetic Engineering Hero - Chapter 3 - Growing E. coli Cells 77
One thing you will notice is that when amino acids are
strung together to form a peptide, the rst amino acid
gets to keep the amine group. An abbreviation for an
amine is N for its nitrogen. This is why the start of the
peptide is called the N-terminus (Figure 3-26). You’ll
also see that the last amino acid in a peptide keeps the
carboxyl group, which has the abbreviation C because
of the Carbon. This is why the end of the peptide is
called the C-terminus (Figure 3-26).
Perhaps the most interesting part of the amino acid
is the “side group”. Think back to Chapter 1: Just as
DNA is made of conserved sugar-phosphate back-
bone (conserved means it is constant and repeating
in DNA), and has a variable “A, T, C, or G” nitrogenous
base - amino acids have a conserved N-C-C backbone
and have a variable “side group”. The side group is
the small cluster of atoms that give each amino acid
a unique characteristic. Amino acid side groups can
be “water-loving” or “water-avoiding”. They can be
positively charged, negatively charged or uncharged.
These different chemical characteristics mean they
can interact with each other and their environment in
many interesting ways. See Figure 3-30 to view differ-
ent amino acids and the side chains drawn in orange.
Using the simplified bonding rules you learned in
Chapter 1 (Table 1-1), think about how the amino acid
chain folds as it is being created by the cell. For exam-
ple, positive and negative charged amino acids will be
attracted to one another. Whereas DNA has comple-
mentary pairs of nucleotides that they must bind to
(A-T, C-G), amino acids do not have “complementary
amino acids” that they must bind to. Rather, general
bonding rules are what cause the amino acid string
to fold up (in-depth discussion about bonding can be
found in Chapter 6 Fundamentals). Recall that opposite
charges attract (+/-) while same charges repel (-/- or
+/+).
In Figure 3-28, you’ll see a simplied example of how
different side chains can interact with one another,
causing attraction or repulsion and ultimately ravel-
ing up into a tight three-dimensional structure. In
Figure 3-28, side groups with a positive charge are
indicated with a ‘+’, those with a negative charge have
a ‘-’, and side groups with no charge are marked by an
‘O’. Following the simple rules, you’ll see that these
different charges drive the interactions. Remember,
non-charged molecules like to interact with other
non-charged molecules. In the real-world example,
a negatively charged amino acid such as glutamate
(Figure 3-30), can interact with a positively charged
amino acid such as lysine (Figure 3-30).
You will learn a lot about the different functions of
proteins throughout this book. If you’re interested in
seeing what a protein looks like, a computer-gener-
ated image can be found in Chapter 6 (Figure 6-17).
Plus charge
Minus charge
No charge
Bonding Interaction
+
+
+
+
+
+
+
+
+
-
-
-
-
-
-
o
o
o
o
o
o
o
o
o
o
o
o
o
Backbone
Side group
Figure 3-28. A string of connected amino acids folds up based on the chemical properties and bonding of the variable side-groups.
Refer back to Table 1-1 to see some simple rules of bonding.
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Zero to Genetic Engineering Hero - Chapter 3 - Growing E. coli Cells 78
Fold-it! Breakout Exercise
How do you think this peptide chain would fold? Apply what you know about hydrophillic and hydrophobic
bonds!
Remember, the solution to these breakout excercises can be found at amino.bio/community
Did you know? There is a game called Fold-it where you get to help the software fold proteins! This in turns
helps scientists apply the resulting protein folding knowledge in their labs. Find it by searching “Fold-it
science” online.
+
o
+
-
o
o
-
+
+
o
H
2
0
H
2
0
H
2
0
H
2
0
H
2
0
H
2
0
H
2
0
?
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Zero to Genetic Engineering Hero - Chapter 3 - Growing E. coli Cells 79
Molecules in your everyday Breakout Activity
You have now started to learn about the molecules that make up the structures of E. coli. You may be inter-
ested to know that you and other organisms are made up of the similar stuff! Go to your cupboard and
fridge to grab a box of cereal and milk. If you don’t have any, use the internet instead. Look at the “Nutrition
Facts” on the packaging. You will see these categories:
Fat - While the term “fat” includes many kinds of molecules, lipids are included in this category. Within
your cereal and milk are lipids that are either from the membranes of formerly living organisms or were
produced and secreted by living cells such as the mammary glands in cows.
Cholesterol - Cholesterol is a molecule made by cells that becomes embedded in the lipid bilayer of the
cell’s membrane. Cholesterol modulates how rigid or exible the membrane is. We did not discuss this, but
E. coli do have cholesterol in their membranes!
Carbohydrate - Carbohydrates make up most of your cereal. These include many different kinds of the
sugars, like the glucose you learned about in Figure 3-18.
Proteins – Many different types of proteins that were involved in helping the organism grow and survive
are left over after the organism has been harvested. These will be broken down into amino acids and reused
by your body to make proteins.
Protein Catalysts in Chemical Reactions Going Deeper 3-7
What do you call something that causes a chemical reaction that otherwise wouldn’t occur? A catalyst. When
you consider the thermodynamics (energy changes) of a chemical reaction, you have to consider the reac-
tants and the energy of the system. This decides whether a reaction will actually take place.
Imagine you’re on a roller coaster and you are a “reactant” - something that will transform into a product
given the right conditions. In this hypothetical roller coaster reaction, you start out as the reactant “antici-
pation and fear”, which, given the right conditions, turns into “exhilaration and fun” (Figure 3-29).
As you’re sitting in the roller coaster car waiting for the ride to start, you are very much “anticipation and
fear”. No matter how long you sit there, you will remain an “anticipation and fear” reactant. However, as
the ride starts and you start to climb higher and higher, energy in the form of “height off of the ground” is
added to the system. You, as “anticipation and fear” remain in that state and your stomach might begin to
churn as the anticipation further builds. Eventually, with enough “height off the ground” energy, you reach
the top of the roller coaster, and as the car lets loose, the roller coaster chemical reaction is in full swing!
There is now enough energy in the system to propel you into the “exhilaration and fun” product state. The
roller coaster falls straight down, your adrenaline explodes, and you SCREAM. Screaming is a by-product
of the roller coaster reaction.
Inner Life of the Cell Video Breakout
Inner Life of the Cell was one of the rst computer generated videos that explored the inner structure of cells.
The creators of the video used information and data from research papers to guide its creation. Find it
online and watch it. It is fascinating (short and long versions with or without narration exist). A key take-
away is that cells are very mechanical and factory-like.
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Zero to Genetic Engineering Hero - Chapter 3 - Growing E. coli Cells 80
1
2
“I’m nervous!”
“That was fun!”
Activation Energy
Reaction happening
Reactant
1 2
“I’m nervous!”
“That was fun!”
Reaction happeningReactant
Enzyme
3
Product
3
Product
Figure 3-29. A normal chemical reaction requires reactants and activation energy needed to cause reactions. Enzymes lower the
amount of activation energy needed and cause reactions to happen in cells that wouldn’t normally happen.
As your roller coaster car returns to the loading area, you have completely transformed into the “exhilaration
and fun” state. All of the anticipation and fear have transformed into feelings of exhilaration and fun. You
also experience some relief, another by-product of the roller coaster reaction. The key parts of the reaction
were the reactants (you as “anticipation and fear”), the energy needed to start the chemical reaction called
the activation energy (height of the roller coaster), and the products (exhilaration and fun, with some scream
and relief). In the case of most chemical reactions that happen in cells, there is not enough activation energy,
usually in the form of heat, in the cells to cause the chemical reaction to occur on its own. This is where
protein enzymes become essential.
Protein enzymes are ‘magical’ macromolecules that can ‘catalyze’ the chemical reaction. This means that
even though there isn’t enough energy, they can still cause the reaction to happen - they have a nifty “hack”
to make the reaction happen. In technical terms, the “hack” is that the enzyme catalyst lowers the ‘activation
energy’ required to cause a chemical reaction. This can catalyze a chemical reaction that wouldn’t normally
happen. In Figure 3-29 this is represented as a tunnel that bypasses the tower.
Each enzyme has a specic purpose and can catalyze a specic chemical reaction. This is what makes biol-
ogy so unique. Thousands of protein enzymes catalyze the chemical reactions necessary for life, including
the creation of enzymes to catalyze more chemical reactions. Chapter 6 covers this in-depth.
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