Chapter 1: Isolating DNA, the Blueprints of Life (3/6)

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22 Zero to Genetic Engineering Hero - Chapter 1 - Isolating DNA, the Blueprints of Life

on completing the rst experiment!

Were you surprised at how much DNA you found in a

single strawberry? You added only a small amount of

DNA to the alcohol, and yet there was a lot of DNA. Now

consider all of the other food you eat - if the food was

at some point living, then it will have DNA in it - you

eat a lot of DNA on any given day!

Now that this experiment is complete, you won’t be

using your isolated DNA further. You can keep it or

throw it away. Since there are no dangerous or living



the toilet/sink and recycle or discard the tubes accord-

ing to your local rules.



several reasons:

• It helped you begin your journey learning about

cells and molecule bonding

• It helped you learn about how to break open cells,

which will be used later in this book to break open

cells that you have genetically engineered

• 

following Fundamentals section, you should keep

remembering the DNA you saw.

Note that genetic engineers do use this technique to

isolate DNA from the environment to use in their proj-

ects. You’ll learn more about this as you become a

Genetic Engineering Hero!

In the following sections, you will take a more in-depth

look at the fundamentals of DNA, and how DNA relates

to cell survival. You’ll also be exploring how DNA can

change naturally or through human intervention. This

will set the stage for later chapters in which you will

start manipulating the genome of cells. Once you have

gone through the rest of this chapter, we recommend

that you go back and repeat the hands-on learning

exercise once more - not only will it reinforce what

you’ve learned, but you will start seeing strawberries,

soap, and salt in a way you never have before.

Book _genetic engineering hero-AUG2021.indb 22Book _genetic engineering hero-AUG2021.indb 22 8/18/21 12:03 PM8/18/21 12:03 PM

23Zero to Genetic Engineering Hero - Chapter 1 - Isolating DNA, the Blueprints of Life

Fundamentals: DNA

Evolution: It’s natural for DNA to

change

All living organisms have DNA. DNA is like the blue-

print or the instructions for a living cell. As you’ll see

throughout this book, in addition to DNA, living cells

are packed full of “nano-machinery” that can read the

DNA and “execute its instructions.” The instructions

embedded in DNA are critical for the cell’s survival.

Cells and DNA can be compared to a computer and its

hard drive. The computer hard drive holds all the

information that is necessary to “run your computer.”

The information is stored as tiny magnetic dots and

dashes in the hard disk. Like Morse code, the little

magnetic dots and dashes are the “language” that the

rest of the computer can understand. Perhaps the

most essential information on the hard drive is the

operating system, like Windows or Mac OS. This infor-



up what you see and hear when your computer boots

up, as well as the software that makes your keyboard,

mouse, screen, webcam, and microphone work. With-

out a hard drive, and the dot and dash information it

contains, your computer would not function.

The computer has many parts other than a hard drive.

These include your screen, keyboard, mouse, cooling

system, graphics, central processing units, battery,

and more. All of these “parts” together are required

to “bring your computer to life” when you press the

power button. The hard drive needs the other

computer parts so that the information stored on it

can be accessed, read, and executed. The computer

parts also need information on the hard drive so they

can operate and communicate with each other. By

changing the dot and dash information in the hard

drive, a computer can behave very differently. Over

the last 40 years, the operating systems of computers

have evolved substantially because they have been

-

opers.

DNA is simply a different medium for storing infor-

mation. Rather than tiny magnetic dots and dashes

on the hard disk, DNA is a microscopic string of tiny

molecules called nucleotides, and it is the order of the

nucleotides that make up the language that the cell

knows how to read. Also, just as the tiny magnetic



changed, so too can the string of molecules that make

up DNA. In other words, DNA can be altered.

In the natural world, DNA can spontaneously change

due to environmental factors, or due to cell malfunc-

tion. Environmental factors like ultraviolet light,

gamma radiation, chemicals in the environment,

viruses, and even molecules produced by other living

organisms can all have an “editing” affect on DNA.



can change how your computer operates (or whether

it will even turn on), a small change such as deleting

some DNA nucleotides can have a profound impact

on a living organism.



permanent chemical. While it is quite stable, DNA is



The changeability of DNA is the basis of evolution. It

is why every organism is unique and why there is

such a fantastic array of living organisms in the world

around you. For billions of years, the nucleotide

sequence making up the DNA of living cells has

changed time after time. DNA nucleotides are

constantly being erased, duplicated, inverted,

jumbled up, and combined with other organisms’

DNA. DNA molecules can even be copy-pasted and

cut-pasted through chemical reactions!

The genetic history of humans is a great example: Did



viruses that once infected our ancestors? An example

of a type of virus that can add its DNA to your genome



is a class of virus called retroviruses. HIV infects

human immune cells, then copies its nucleic acid into

human cells so that these human cells will keep this

new DNA and make more of the virus. This shows that

human DNA has not been solely human since “the

beginning.” Rather it is the accumulation of DNA from

different organisms in nature as well as natural

changes to the DNA sequence over time. When enough

DNA is transferred, duplicated, removed, or other-



and behaves differently from its parent.

It can take thousands, millions or billions of genera-

tions for changes in DNA to accumulate to the point

where an organism becomes unique. When minor

DNA changes happen even one thousand times, the

“Great-one-thousandth Grandparents” can look very

different than its “Great-one thousand Grandchild.” It

may even result in a different species! Let’s write this

out so you can see what 1000 generations look like:

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24 Zero to Genetic Engineering Hero - Chapter 1 - Isolating DNA, the Blueprints of Life

Great great great great great great great great great great great great great great great

great great great great great great great great great great great great great great great

great great great great great great great great great great Grand Parent.

That is a lot of grandparents! Do you know who your

great-one thousand grandparents were? Do you think

they looked just like your grandparents? In humans,







in days. Considering that a microorganism’s lineage

goes back billions of years, that provides a lot of

opportunities for generations to change and evolve.

Life on earth started with the simplest of life forms,

with simple DNA blueprints. Through billions of years

and an unimaginable number of incremental changes

to the DNA blueprint, we now see countless species of

microorganisms, plants, fungi, insects, and mammals

such as humans.

Modern Synthesis

While the understanding of DNA, genetics, and hered-

ity matured over hundreds of years, an essential

milestone occurred in the early 20th century as

Darwinian evolution and Mendelian genetics transi

tioned from theory to fact. The combining of

Darwinian evolution (natural selection) and Mende-

lian genetics (inherited DNA) was termed the Modern

Synthesis.

Today, Gregor Mendel is known as the founder of

genetics, and genetics, of course, is the foundation of

  



traits are passed on from one organism to the next,



traditional breeders of livestock and crops had been

slowly modifying organisms over at least thousands



that biology could be changed through domestication

had yet to be achieved.

It wasn’t until Mendel started his pea plants experi-

ments that crucial information on genetics emerged

(Figure 1-10). Mendel found that when he cross-polli-

nated pea plants with different colored seeds, some

of those seed colors were preferentially passed down

to the next generation of plants. But, looking further

down the line of pea plant generations, he found that

some seed colors eventually re-emerged! His experi-

      

experiments, went something like this:

1. Yellow seed pea plants were carefully bred with

other seeded yellow pea plants to ensure he had

“pure-breed” yellow pea plants.

2. The same was done with green seed pea plants.

3. Yellow and green seed pure-bred plants were

then carefully cross-pollinated. This is quite easy

to do. Today, you can use a Q-tip and gently rub a

blossom of one plant to gather pollen, then rub it

in another plant blossom, and lastly, rub it back



4. The plants grew, matured, and produced seeds

       

for similar future experiments.

Book _genetic engineering hero-AUG2021.indb 24Book _genetic engineering hero-AUG2021.indb 24 8/18/21 12:03 PM8/18/21 12:03 PM

25Zero to Genetic Engineering Hero - Chapter 1 - Isolating DNA, the Blueprints of Life

The pure-bred plants would always produce the

expected colored seeds: yellow produced yellow

seeds and green produced green seeds. However,





were yellow! It looked as though some genetic infor-

mation for yellow seeds was preferred over green

(Figure 1-11)!

But, things ended up getting a bit more complicated.

-

ation yellow seeds were grown into plants and

cross-bred? You might expect this preferential yellow

genetic information to cause only yellow seeds. But

the result included the reemergence of green seeds!

And the most interesting part was they appear in a

ratio of one green seed for every three yellow seeds.

       

derived information about how traits were passed

down from a parent to its offspring was available. It



rules” for which information is passed to the offspring.

To explain this, Mendel coined the terms “recessive”

and “dominant” genes. The green seeds were the

ones with the recessive trait and the yellow seeds the

dominant trait.

Mendel’s studies broadened beyond seed color into

different plant traits, including height, blossom

colors, pea pod shapes, colors, and more. In these

studies, he found other “genetic rules” existed! Today,

our hair color, eye color, skin color, and a lot more are

well-known examples of how genetics are passed

down from parents to offspring.

Modern synthesis combined Darwinian evolution

     



how biological organisms can change through time.

Mendelian genetics, now just genetics, turned out to

be the mechanism or the “how” and “why” different

genetic material is passed down from parent to

offspring. Darwinian evolution allowed scientists to

see that genetics applied to all organisms, not just pea

plants. Modern synthesis also included some other

key mechanisms in which DNA changes occur in

organisms and populations:

Mutations: when changes in the DNA sequence

happen due to copy errors. While mutations can be

increased due to environmental factors, this is

often considered independent of selective environ-

mental pressures (natural selection). In most cases,

mutations are harmful to an organism; however, in



that can help an organism survive in their environ-

ment. In other words, mutations do occur randomly

but can become a part of natural selection.

Random genetic drift: is where allele frequency

changes in populations. An allele is a DNA sequence

(e.g. gene) that is very similar to another allele but

has a slightly different sequence. Alleles are created

due to mutations. As organisms reproduce, these

different versions of DNA sequences will “move”

through a population. Similar to the pea experi-

ments above where the “yellow seed” and “green

seed” alleles “moved” through the pea population

as the plants were bred.

 is where allele frequency changes due

to immigration or emigration to/from a population.

For example, if there were only true-bred green

seed pea plants in a region and a person or bird

happened to bring a yellow pea seed to that region.

When that pea plant grows, it’s yellow seed allele

will become dominant in the region in the coming

years as cross-breeding occurs.

A key basis for natural selection, random genetic drift,



and result in different DNA sequences (alleles). While

most mutations negatively impact an organism, some



help an organism survive in a particular environment

(natural selection) or can help the organism survive

independent of the environment. The alleles can then

“move” around and change a population through gene

        

generation, mutations reshape us, and the world

around us as species change or new species emerge.

Figure 1-10.

Book _genetic engineering hero-AUG2021.indb 25Book _genetic engineering hero-AUG2021.indb 25 8/18/21 12:03 PM8/18/21 12:03 PM

26 Zero to Genetic Engineering Hero - Chapter 1 - Isolating DNA, the Blueprints of Life

Genetic engineering: The road to

precise editing of DNA



DNA in organisms for thousands of years through

domestication and selective breeding. You can see

the outcomes of these actions in our homes, farms,

and factories. These methods of changing the DNA of

living organisms take advantage of evolution. When

humans cross-breed plants, the DNA within the

plants mix: DNA from one plant will combine with





human intervention, however, if the new trait is bene-



for because the plant’s survival will be encouraged by

humans through watering, and propagating the

plant’s seeds. Because of this, plants, especially crop

-

able when compared to their ancestors (Figure 1-12).

Domestication and selective breeding do not only

apply to crops. Consider pets for a moment. The “orig-

inal dog” is Canis lupus, better known as the wolf. Dogs

have been so extensively bred by humans that a huge

dog such as a Great Dane—standing at a minimum of



physically mate and reproduce in nature with a small

dog such as a Chihuahua—standing at less than 1 foot

and weighing less than 10 pounds. The Chihuahua is



descendants from the same source DNA (Figure 1-13).

In the natural world, these two organisms can no

longer effectively breed. Their DNA can no longer

combine and intermix as would naturally happen in

a species. Without human intervention, this will

eventually lead to the development of two different

species. This is evolution in progress.

The methods in which humans evolve plants and pets

through deliberate breeding and selection extends

into all corners of the natural world - trees, grasses,



Much of the food we eat today was evolved through

selective breeding by humans. This process often

takes a long time because “DNA mixing” through

these methods is random, and desirable traits only

appear by chance. What if randomness could be taken

out of the equation? What if humans could, with

extreme precision, edit DNA?

The precise engineering of organisms is the focus of

this book. By its end, you will have gone through exer-

cises where you will have precisely changed an

organism’s DNA to get a desired trait. Over the past

100 years, humans have made ground-breaking

discoveries that have led us to understand what DNA

is, how DNA behaves, and its importance in biology.

These discoveries have led to new technologies that

enable us to precisely read, write and edit the DNA of

organisms. There has also been a change in the mind-

set of people. No longer is nature and the natural

world seen as being immovable or unchangeable. A

robust engineering discipline has emerged where we

can now make very important things using biology.

We call this the Biology-as-a-Technology mindset.

The knowledge and skills imparted by this book are

not to be taken lightly. Understanding how DNA and

cells interact will be vital to making informed deci-

sions about using your new skills. Now that you have

seen DNA and know that it can be manipulated let’s

further explore the building blocks of DNA and the

cells where they reside.

Figure 1-11. Mendel’s pea plants experiment provided the

basis for modern genetics.

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Table of Contents for Chapter 1: Isolating DNA, the Blueprints of Life (3/6)

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Table of Contents for
Chapter 1: Isolating DNA, the Blueprints of Life (3/6)