106 Zero to Genetic Engineering Hero - Chapter 4 - Genetic Engineering Your E. coli Cells
What is a gene?
A gene is one of the most talked about, but least
understood, topics in education. A gene is a length
of DNA that has all the DNA sequence the cell needs
to read and begin the Three Steps to Microfacturing. In
other words, a gene is a length of DNA that results in
the creation of an end-product that has a function,
like RNA or a protein.
This means a gene must have information embedded
in the DNA sequence to start and stop the Three Steps
to Microfacturing and to create a cellular product with
a function. In other words, a gene is a length of DNA
that can tell the cell machinery (RNA polymerase)
when and where to start the Three Steps to Microfactur-
ing as well as what to make. Let’s look deeper at how
Just like a sentence has a structure or “syntax”, such
as a subject-verb-object, genes have a grammati-
cal order. Two kinds of information are stored in a
gene’s DNA sequences. They are called “non-coding
sequences” and “coding sequences” (Figure 4-23).
These are both just plain old DNA. The RNA poly-
merase is able to distinguish between them.
A non-coding DNA sequence is a segment of DNA
that acts as a switch, controlling when and how much
product is made from the gene. The non-coding
sequence has the right characteristics to bind ‘tran-
scription machinery’, and it acts as the starting point
of transcription. Consider The Four B’s of Cell Opera-
tion: Bump, Bind, Burst, Bump. If the non-coding DNA
sequence is unable to bind the transcription machin-
ery, then transcription doesn’t happen. Conversely,
if the DNA sequence has the right shape and charge
to bond to the transcription machinery, RNA poly-
merase binds to the DNA more frequently, and
transcription can occur.
In the hands-on exercise, you engineered your cells
by adding a DNA plasmid that contains a gene for
creating protein color pigments. Within that gene is
a non-coding sequence designed to bind with a cell’s
transcription machinery ~12 hours after the cells
start growing and keep transcribing it thereafter.
A coding DNA sequence is a sequence situated imme-
diately next to the non-coding DNA. It is read and
transcribed by the transcription machinery into RNA.
The coding DNA sequences are like the designs for
the functional end-product that will be made from
the gene. The non-coding DNA sequences are like
the switch telling the cell where and how frequently
to transcribe the coding DNA sequence.
How does the cell know how to start transcription?
Both the DNA and transcription machinery are
bumping around the cell. If the non-coding DNA
sequence has the ‘right’ shape and chemical bonding
properties, it will bind to the transcription machinery,
enabling transcription to start. Let’s get more specic.
Small proteins called sigma factors complete the
Four B’s and eventually bind to short non-coding DNA
sequences within genes. For transcription, the small
non-coding regions are called promoters (Figure
4-23) because they “promote” the transcription of
the gene. Promoters are the starting points of tran-
scription, which means they are the starting point of
a gene. The sigma factor (σ) has a particular size and
shape that is able to bind to a specic DNA sequence.
Once a sigma factor binds to the promoter of a gene,
it then binds to the RNA polymerase. In other words,
the sigma factor acts as a bridge between the DNA
and the RNA polymerase, the enzyme that transcribes
Once RNA polymerase is bound to the promoter
region via the sigma factor, the RNA polymerase
creates a short RNA sequence called the initiation
sequence, which locks the RNA polymerase to the
DNA (4-23ii). The RNA polymerase then “drives off”
and escapes the promoter to begin unzipping, read-
ing, and transcribing the coding DNA sequence into
An analogy can be drawn between transcription and
drag car racing (do a quick video search for ‘drag car
racing’). Note the similarity:
• Step 1: A race track ofcial walks onto the starting
line (a sigma factor binds to the promoter, which is
the ‘start line’ of the gene).
• Step 2: The ofcial waves the car forward and the
car advances to the starting line (the sigma factor
‘recruits’ and binds to RNA polymerase at the
• Step 3: The car does a ‘burn out’, spinning its tires
to heat them up, making the tires nice and sticky,
so it has more traction (the RNA polymerase makes
a short RNA initiation sequence, locking into the
• Step 4: Green light! The race car oors it and takes
off from the starting line (RNA polymerase leaves
the promoter and commences transcription).
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