8

Biotechnology
Quarter 3 – Module 1:

DIVISION OF ANGELES CITY

Tools Used in Genetic
Engineering
Biotechnology – Grade 8
Alternative Delivery Mode
Quarter 3 – Module 1-2: Tools Used in Genetic Engineering
First Edition, 2021

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 8
Biotechnology
Quarter 3 – Module 1:
Tools Used in Genetic
Engineering
Introductory Message
This Self-Learning Module (SLM) is prepared so that you, our dear learners,
can continue your studies and learn while at home. Activities, questions,
directions, exercises, and discussions are carefully stated for you to understand
each lesson.

Each SLM is composed of different parts. Each part shall guide you step-
bystep as you discover and understand the lesson prepared for you.

Pre-tests are provided to measure your prior knowledge on lessons in each

SLM. This will tell you if you need to proceed on completing this module or if you
need to ask your facilitator or your teacher’s assistance for better understanding
of the lesson. At the end of each module, you need to answer the post-test to
selfcheck your learning. Answer keys are provided for each activity and test. We
trust that you will be honest in using these.

In addition to the material in the main text, Notes to the Teacher are also
provided to our facilitators and parents for strategies and reminders on how they
can best help you on your home-based learning.

Please use this module with care. Do not put unnecessary marks on any
part of this SLM. Use a separate sheet of paper in answering the exercises and
tests. And read the instructions carefully before performing each task.

If you have any questions in using this SLM or any difficulty in answering
the tasks in this module, do not hesitate to consult your teacher or facilitator.

Thank you.
 What I Need to Know

This module was designed and written with you in mind. It is here to help
you familiarize the different tools used in genetic engineering. The scope of this
module permits it to be used in many different learning situations. The language
used recognizes the diverse vocabulary level of students. The lessons are
arranged to follow the standard sequence of the course. But the order in which
you read them can be changed to correspond with the textbook you are now
using.

The module is summated into one lesson, namely:

● Lesson 1 – Tools Used in Genetic Engineering

After going through this module, you are expected to describe the different tools
used in genetic engineering.
 What I Know

Directions: Read each question carefully. Choose the letter of the correct
answer.

1. The term is defined as the basic physical and functional unit of heredity.
a. alleles c. genes
b. deoxyribonucleic acid d. ribonucleic acid
2. It is a branch of science that is concerned how various traits are inherited.
a. biological engineering c. heredity
b. genetics d. pathology
3. The process by which recombinant DNA technology is utilized to alter the
genetic makeup of an organism.
a. biological engineering c. genetic engineering
b. biological modification d. genetic modification
4. When did Hindll isolate the first restriction enzyme?
a. 1960 c. 1990
b. 1980 d. 1970
5. It is the first organism used in DNA technology experiments.
a. E. coli c. S. cerevisiae
b. E. faecalis d. S. typhimurium
6. This is a laboratory technique used to amplify a single copy or a few copies of
a segment of DNA across several orders of magnitude, generating thousands
to millions of copies of a particular DNA sequence.
a. Agarose Gel Electrophoresis c. Polymerase Chain Reaction
b. Molecular Scissor d. Restriction Endonuclease
7. The enzymes that make one incision on each of the two strands of DNA at
specific locations based on the nucleotide sequence are known as
______________.
a. DNA Polymerase I c. Primase
b. Helicase d. Restriction Endonuclease
8. He discovered the Polymerase Chain Reaction.
a. Hamilton Smith c. Kary Mullis
b. Hindll d. Werner Abner
9. It is a branch of biotechnology that deals with the study and investigation of
genomic information from trace evidence found at crime scenes. Agricultural
a. biotechnology c. Industrial biotechnology
b. Forensics biotechnology d. Medical biotechnology
10. It is a technique commonly used in laboratories to separate charged
molecules like DNA, RNA and proteins according to their size.
a. Gel Electrophoresis c. Polymerase Chain Reaction
b. Molecular Scissor d. Selection of Prokaryotic Host
Lesso
n The Different Tools Used in
1 Genetic Engineering

What’s In

Our previous module learned that mutation could result from DNA copying
mistakes during cell division, exposure to ionizing radiation, exposure to
chemicals called mutagens, or infection by viruses. The majority of mutations
have neither negative nor positive effects on the organism in which they occur.
These mutations are called neutral mutations. While there is a mutation with
positive effects, a mutation can develop resistance to some diseases like
atherosclerosis. These mutations are called beneficial mutations. Lastly, a
harmful mutation can cause genetic disorders and diseases such as cancer and
cystic fibrosis.

ACTIVITY 1
Direction: Match the types of mutation to their genetic codes and write the letter
of the correct answer before each number.

TYPES OF MUTATION GENETIC CODES

1. Duplication A.

2. Inversion B.

3. Normal Sequence C.

4. Deletion D.
 5. Insertion E.

ACTIVITY 2
Direction: Fill in the diagram with the different types of mutation.
(Note to the learners: You may draw the illustrated diagram on your answer
sheet.)

Mutation
 What’s New
Direction: Match each tool used in genetic engineering to its corresponding
description. Choose the letter of the correct answer.

Answer Genetic Tools Description

1. Molecular Scissor a. It multiplies the DNA
exponentially for each of the 25
to 75 cycles.
2. Polymerase Chain
Reaction b. It is the enzymes that cut
DNA at specific locations based
on the nucleotide sequence.
3. Gel Electrophoresis
c. It monitors the changes in
protein content in body fluids

d. The utilization of multi-cell

4. Polymerases organisms to produce human
proteins since these hosts with
complex structures are more
suitable for synthesizing complex
5. Eukaryotic Host proteins.

e. The groups of enzymes

that catalyze the synthesis of
nucleic acid molecules

What do you think are these tools for in genetic engineering?

What is It

You may have heard about genetic engineering in newspapers, TV shows,

and the Internet. Sci-fi movies like X-Men and Splice depict individuals with
enhanced genetic modifications that give them special abilities.
So, what exactly is Genetic Engineering? Genetic engineering involves
manipulating genetic material (DNA) to achieve the desired goal in a
predetermined way. In history, one of genetic engineering’s breakthroughs was
the successful discovery of CRISPR/Cas9, which was used nowadays as an editing
tool to modify genomes—a trailblazing development for medicinal purposes
curing genetic disorders in the near future. Furthermore, genetic engineering
also made cloning possible as it successfully cloned a mammal from an embryo
cell, a sheep named “Dolly,” and Ian Wilmut and his colleagues executed the said
cloning.
However, what are the standard tools used in genetic engineering?
Moreover, how does genetic engineering help in the detection of viruses?

Figure 1: Genetically Modified Organisms and Tools Used in Genetic Engineering.

Genetic Engineering Defined

The term genetic Engineering is initially referred to various techniques used for
the modification or alteration of organisms through the processes of heredity and
reproduction.
Increasing plant and animal food production, diagnosing and treating diseases
through medical advancement, and producing useful drugs and vaccines for the
Sars-Cov2, are the major focus on the importance of genetic engineering.

THE DIFFERENT TOOLS USED IN GENETIC ENGINEERING

Here are tools that are commonly used in genetic engineering:
● Polymerase Chain Reaction (PCR) is efficient technique because it
multiplies the DNA exponentially for 25 to 75 cycles. A cycle takes only a
 minute, and each new segment of DNA that is made can serve as a template
for new ones. This technique is used in molecular biology to amplify a single
copy or a few copies of a segment of DNA across several orders of
magnitude, generating thousands to millions of copies of a particular DNA
sequence. Developed in 1983 by Kary Mullis, PCR is now a common
technique used in clinical and research laboratories for various applications
(Javed, 2017).

Figure 2: Polymerase Chain Reaction

Image Source: https://explorebiotech.com/10-tools-for-genetic-engineering/

● Restriction Enzymes (Molecular Scissor) are enzymes that create one

incision on each of the two strands of DNA at specific locations based on the
nucleotide sequence. DNA cut with a restriction enzyme produces many
smaller fragments of varying sizes. These can be separated using gel
electrophoresis or chromatography. Furthermore, hundreds of different
restriction enzymes isolated from many different bacteria strains are capable
of cutting DNA at a distinct site. Restriction Enzymes was isolated in 1970 by
Hindll. He also did the subsequent discovery and characterization of
numerous restriction endonucleases (Hitendra, 2018).
 Figure 2: Restriction Enzymes
Image Source: https://explorebiotech.com/10-tools-for-genetic-engineering/

● Gel Electrophoresis is used for various purposes, from viewing cut DNA to
detecting DNA inserts and knockouts. It is also used to estimate the
molecular weight of protein and nucleic acids, purification of isolated
proteins, monitoring changes of protein content in body fluids, blotting
application, and many more. Purifying DNA from cell culture or cutting it
using restriction enzymes would not be of much use if we could not visualize
the DNA that is, find a way to view whether or not your extract contains
anything or what size fragments you have cut it into. One way to do this is by
gel electrophoresis (Tapeshwar, 2015).

Figure 3: Gel Electrophoresis

Image Source: https://explorebiotech.com/10-tools-for-genetic-engineering/
● DNA Ligase are enzymes that can create covalent bonds between
nucleotide chains. The enzymes DNA polymerase I and polynucleotide kinase
are also crucial in filling in gaps, or phosphorylating the 5′ ends, respectively.
The DNA ligase used in molecular cloning differs in their abilities to ligate
noncanonical substrates, such as blunt-ended duplexes DNA: RNA hybrid or
ss DNAs. In genetic research, DNA Ligase are often utilized to link two or
more individual strands of DNA, to create a recombinant strand, or close a
circular strand that has been cut with restriction enzymes (Faraza ,2017).

Figure 4: DNA Ligation Process

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● According to Faraza (2017), polymerases are collectively referred as the

groups of enzymes that catalyze nucleic acid molecules’ synthesis. It is
customary to use the name of the nucleic acid template on which the
polymerase acts. The three critical polymerases are given below.

Figure 5: Polymerizing and Proofreading

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o DNA-dependent DNA polymerase that replicates DNA from DNA.

 o RNA-dependent DNA polymerase (reverse transcriptase) that transcribes
DNA from RNA. o DNA-dependent RNA polymerase that transcribes RNA
from DNA

Figure 6: Plasmid Map

Image Source: https://explorebiotech.com/10-tools-for-genetic-engineering/

● Prokaryotic Host are able to multiply their plasmids (along with foreign
DNA) also multiply to produce millions of copies, referred to as a colony or in
a short clone. The term ‘clone’ broadly refers to a mass of cells, organisms,
or genes that results from the multiplication of a single cell, organism, or
gene. Furthermore, the bacteria Escherichia coli, was the first organism used
in the DNA technology experiments and continues to be the host of choice by
many workers. Undoubtedly, E.coli, the simplest Gram-negative bacterium (a
common bacterium of human and animal intestines), has played a key role in
the development of present-day biotechnology. Under a suitable
environment, the number of E. coli can double every 20 minutes
(Faraza ,2017).

• Eukaryotic Host are preferred to produce human proteins since these hosts
with complex structures (with distinct organelles) are more suitable to
synthesize complex proteins. The most commonly used eukaryotic organism
is the yeast, Saccharomyces cerevisiae. It is a non-pathogenic organism
routinely used in the brewing and baking industry. Certain fungi have also
been used in gene cloning experiments (Faraza ,2017).

● Selection of Small Self-Replicating DNA

 Small circular pieces of DNA that are not part of a bacterial genome, but are
capable of self-replication, are known as plasmids. Plasmids are often used
as vectors to transport genes between microorganisms. In biotechnology,
once the gene of interest has been amplified and restriction enzymes cut
both the gene and plasmid, they are ligated together, generating what is
known as recombinant DNA. Viral (bacteriophage) DNA can also be used as a
vector, as can cosmids, recombinant plasmids containing bacteriophage
genes (Faraza ,2017).

Figure 7: Plasmid Map

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● Methods to Select Transgenic Organisms

According to Faraza (2017), not all cells will take up DNA during
transformation. Therefore, it is essential to identify the cells that transform
and those that have not. Generally, plasmids carry genes for antibiotic
resistance, and transgenic cells can be selected based on the expression of
those genes and their ability to grow on media containing that antibiotic.
Alternative selection methods depend on the presence of other reporter
proteins such as the x-gal/lacZ system or green fluorescence protein, which
allow selection based on color and fluorescence, respectively.
 Figure 8: Selection of Transgenic Organisms
Image Source: https://explorebiotech.com/10-tools-for-genetic-engineering/

What’s More

Activity 1: Jumbled Letters!

Direction: Arrange the jumbled letters to determine the tools used in genetic
engineering and write a brief description about them.

1.DISPALM 6. ESEGN

2.GTECNIE GEGENINERIN 7. DAN SIGALE

3.EGL TECLOROPESERHIS 8. SAEMPLOYERS

4.ROLAMECUL CISSROSS 9. TASYE

5.SEPAROELMY CAHIN NEROCATI 10. OAREGAS

Assessment 1
1. What is DNA Ligase? And how is it used in genetic engineering?
2. How is the Polymerase chain reaction useful in the detection of viruses?
3. Why are genes functional in genetic engineering?

Activity 2: Match Up!

Direction: Identify what is asked for each item by choosing the letter of the
correct answer in the box.
a. DNA-dependent RNA polymerase f. Restriction Enzymes
b. Hindll g. Kary Mullis
c. PCR h. Saccharomyces cerevisiae
d. Escherichia coli i. RNA-dependent DNA polymerase
e. Plasmids j. Gel Electrophoresis

1. These are enzymes that can create covalent bonds between nucleotide
chains.
2. It is the most commonly used eukaryotic organism.
3. It is considered as a common bacterium of the human and animal
intestines.
4. It is the enzyme that transcribes RNA from DNA.
5. It is used to monitor the changes of protein content in body fluids.
6. These are enzymes used to cut DNA at specific locations based on the
nucleotide sequence.
7. It is a genetic engineering tool used to multiply the DNA exponentially for
each of the 25 to 75 cycles.
8. He discovered the PCR.
9. He isolated the first restriction enzyme in 1970.
10. These are enzymes that transcribe DNA from RNA

Assessment 2
1. How were restriction enzymes discovered?
2. Why is yeast the most commonly eukaryotic organism used for gene cloning
experiments?
3. How are the tools genetic engineering beneficial in medicine today? Justify
your answer.

Activity 3: Step Up!

Direction: Using letters A, B, and C, arrange the stages/steps on how the
different techniques/tools in genetic engineering work.

1. MAKING A RECOMBINANT DNA

_____ Sticky ends are joined by DNA ligase
_____ Restriction enzymes cut the desired DNA sequence
_____ Study and determine the specific gene needed

2. POLYMERASE CHAIN REACTION / MAKING DNA COPIES

_____ DNA polymerase starts making copies
 _____ “primers” provide a lace for DNA polymerase
_____ DNA is heated to separate the strands and cooled to bind
3. TRANSFORMING BACTERIA
_____ Insert a human gene into plasmid / bacterial DNA
_____ The recombinant DNA is inserted in the bacterial cell
_____ The bacteria can produce the human protein
4. TRANSFORMING PLANT CELLS
___The plasmid can be used to infect plant cells that take up DNA on its
own
___ Insert a piece of foreign DNA into the plasmid
___ Inactivate the tumor-producing gene of a bacterium
5. TRANSFORMING ANIMAL CELLS
____ The host gene may lose (knocked out) sequences in between
____ DNA molecule is constructed with two ends that may recombine with
specific sequences
____ The knocked-out gene is replaced with a new gene

Assessment 3
1. What is PCR? And how is the process of making DNA copies performed?
2. How is human insulin produced by genetically modified bacteria? Describe
the process and determine what tool in genetic engineering was used.
3. How is recombitant DNA generated?

Activity 4: Let’s Investigate

Direction: Read the case of Jesse Gelsinger and answer the questions.

THE CASE OF JESSE GELSINGER

For 9 years, gene therapy seemed to promise cures to incurable genetic
disorders. Then in 1999, a gene therapy experiment failed. Jesse Geisinger, 18
years old, had ornithine transcarboxylase (OTC) deficiency, a rare metabolic
disorder that causes a build-up of ammonia. He was able to control the disease
with a low-protein diet and 32 pills per day. Although he was otherwise healthy at
the time, he signed up for an experimental trial at the University of Pennsylvania
that would benefit babies born with a fatal form of OTC.
The experiment was to test the safety of treatment and to determine the
maximum tolerated dose of an adenovirus vector with the OTC gene. Four days
after he received an infusion into his liver of recombinant virus, he died from
complications resulting from a clotting disorder and organ failure due to the
adenovirus. Interestingly, three monkeys had died of the same problem after
they received a stronger version of the adenovirus at a dose 20X higher than any
of the doses later used in the human experiment. Nevertheless, the experiment
proceeded.
In 2003 nearly 30 gene therapy trials were canceled after two children treated
for ADA deficiency developed leukemia in a French trial. It was discovered that
the retrovirus had inserted next to an oncogene in a white blood cell to grow
uncontrollably, causing leukemia. The children were treated with chemotherapy.
These cases raise issues about gene therapy safety, although some experts say
the development of leukemia may have been specific to the SCID gene therapy
trials.
Guide Questions:
1. What is gene therapy?
2. Do you agree that gene therapy may be the best method to treat ailments
such as cancer, AIDS, and genetic disorders? Explain.

Assessment 4
1. One of your siblings has a genetic disorder, and you were offered to
undergo clinical trials for free. Will you allow your sibling to undergo gene
therapy? Explain.
2. If you were a biologist, how would you address gene therapy safety issues
with possible patients?

Activity 5: DNA Fingerprinting Analysis

Case 1
Mr. Chan’s family consists of mom, dad and four kids. The
parents have one daughter and one son together, another
daughter is from the mother’s previous marriage, and the other
son is adopted. Here are the DNA analysis results:

1. Which
child is

adopted? Why?
2. Which child is from the mother’s previous marriage? Why?
3. Who are the own children of Mr. and Mrs. Chan?

Assessment 5
1. What is DNA Fingerprint Analysis?
2. How does rep-PCR relate to DNA fingerprinting?
3. How does pulsed-field gel electrophoresis relate to DNA fingerprinting ?
Activity 6: Crime Investigatory
Direction: Read the short article about Grace Hayden and answer the following
questions.
A single fingerprint and the actions of an “above and beyond” deputy led
investigators to arrest a man in North Carolina for allegedly murdering an elderly
woman 31 years ago in California, according to officials. Grace Hayden, 79, was
raped and killed in San Diego in May 1987, said Investigator Erich Hackney of the
Robeson County, North Carolina, District Attorney’s Office. San Diego District
Attorney Investigator Tony Johnson was reviewing Hayden’s brutal unsolved
killing when he found a single fingerprint from a left ring finger on Hayden’s
 kitchen stove, Hackney said in a news release. “Johnson resubmitted the
fingerprint through the national fingerprint database,” Hackney said, and found a
match to 62-year-old Kevin Ford in Robeson County, North Carolina. When that
warrant was served in 2015, Robeson County Sheriff’s Office Deputy John Blount
happened to decide to fingerprint Ford -- “something rarely done on a charge of
this nature,” according to Hackney. “It was this set of fingerprints that were
taken by Blount that matched the print left by Ford at the crime scene,” Hackney
said.
A DNA sample was obtained from Ford to compare, and investigators found that
it matched DNA collected from the victim, Hackney said.
Source: abcnews.go.com
Guide Questions:
1. Should fingerprints be used as evidence? Why?

Assessment 6
1. How are fingerprints used to solve crimes?
2. In your perspective, are fingerprints valid enough to convict a person?
Why?

What I Have Learned

Let’s sum up what you have learned. Read each item carefully. Complete its
meaning by supplying the correct term.

1. Gel electrophoresis, molecular scissors, and polymerase chain reaction, are

the common tools used in _____________.
2. The process by which recombinant DNA technology is utilized to alter the
genetic makeup of an organism is called _____________.
3. It is a technique commonly used in laboratories to separate charged molecules
like DNA, RNA and proteins according to their size, known as __________.
4. These are enzymes that make one incision on each of the two strands of DNA
at specific locations based on the nucleotide sequence, namely __________.

5. It is a laboratory technique used to amplify a single copy or a few copies of a

segment of DNA across several orders of magnitude, generating thousands to
millions of copies of a particular DNA sequence, known as ____________.
6. The branch of biotechnology that deals with the study and investigation of
genomic information from trace evidence found at crime scenes is called
____________.
7. Genes is the basic physical and functional unit of __________.
8. The branch of science that is concerned with how various traits are inherited is
called ___________.
9. It is an impression left by the friction ridges of a human finger that serve as
valid evidence in crime scenes, known as __________.
10. The genetic tool used to detect people with COVID-19 virus is ___________.

What I Can Do
Practical Use of Genetic Engineering During the COVID-19
Pandemic
During the 2020 Pandemic, COVID-19 affects
the lives of many people and slows down the global
economy. This pandemic has killed almost 1.79
million worldwide. The most common symptoms of
this viral infection are fever, cold, cough, bone pain,
and breathing problems, which will lead to
pneumonia.
In response, the health department utilized COVID-
19 rRT-PCR test as a real-time reverse transcription
polymerase chain reaction (rRT-PCR) test for the
qualitative detection of nucleic acid from
SARS-CoV-2 in upper and lower respiratory Retrieved from:
https:// images .app.goo.gl/miNE5
specimens (such as nasopharyngeal or BWtqcovJkU99
oropharyngeal swabs, sputum, lower respiratory
tract aspirates, bronchoalveolar lavage, and nasopharyngeal wash/aspirate)
collected from individuals suspected of COVID-19 by their healthcare provider
(HCP), as well as upper respiratory specimens (such as nasopharyngeal or
oropharyngeal swabs, nasal swabs, or midturbinate swabs) collected from any
individual, including for testing of individuals without symptoms or other reasons
to suspect COVID-19 infection.
In addition, the technological advancement of
genetic engineering gave us the pathway for the
availability of vaccines with different efficiency in
some countries, yet there are still side effects once
you are vaccinated.
As a student, what is your greatest learning
from this module? And how can you respond to the
COVID-
19 outbreaks?

Retrieved from: https://images.app.goo.gl/iLR i8ZwkNv4tFkUv9

Assessment

Directions: Read each question carefully. Choose the letter of the correct
answer.
1. What do you call an organism that contains genes from two different
organisms?
a. Altered genome organism
b. Mutant organism
c. Modified organism
d. Transgenic organism

2. Which of the following best describes the use of genetic engineering?

a. alter the genetic makeup of an organism
b. generate new hybrid strains
c. improve disease resistance
d. all of the above

3. Which of the following is the most challenging issue facing genome

sequencing or organism modification?
a. the availability and stability of DNA
b. the ethics of using information from genomes at the individual level
c. the inability to develop fast and accurate sequencing or modifying
techniques.
d. all of the above

4. What carries a gene from one organism into a bacterial cell?

a. a plasmid
b. a restriction enzyme
c. electrophoresis gel
d. polymerase chain reaction

5. When was the Polymerase Chain Reaction discovered?

a. 1963
b. 1973
c. 1983
d. 1993
True or False. Write the word “True” if the statement is correct and write
“False” if the statement is incorrect.

1. Dolly the sheep was the first mammal cloned from an embryo cell.
2. Generally, it is easier to insert genes into plant, yeast, and bacteria cells,
rather than animal cells, rather than animal cells.
3. Criminology is another term for forensic science.

4. . The use of DNA as a forensic tool began in the 1980s.

5. Gene therapy is a medical technique to treat or prevent disease.

Additional Activities
 Directions: Make an editorial cartoon showing how the tools are used in genetic
engineering which are beneficial to humans in terms of health, agriculture, and
technology. Use the rubric below as your guide in your illustration.

EDITORIAL CARTOON RUBRICS

CATEGORY 4 3 2

Required The cartoon All required All but one (1) of

Elements includes all elements are the required
required included in the elements are
elements as well cartoon. included in the
as cartoon.
additional
information.
Labels All items of Almost all items of Many items of
importance on the importance on the importance on the
cartoon are cartoon are clearly cartoon are clearly
clearly labeled. labeled. labeled.
Graphics- All graphics are All graphics are All graphics relate to
Relevance related to the related to the topic the topic
topic and make it and most make it
easier to easier to
understand. understand.
Attractivene The cartoon The cartoon is The cartoon is
ss is attractive, in terms acceptably
exceptionally of design, layout, attractive though it
attractive, in and neatness. may be a bit messy.
terms of design,
layout, and
neatness.
Grammar There are no There 1-2 There 3-4
grammatical/ grammatical/ grammatical/
mech anical mechan ical mechan ical
mistakes in the mistakes in the mistakes in the
cartoon. cartoon. cartoon.