8

Biotechnology
Quarter III – Module 1:
Tools of Genetic Engineering

"Designed by macrovector / Freepik"

Biotechnology – Grade 8
Self-Learning Module
First Edition, 2020

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Published by the Department of Education – Regional Office VIII

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Assistant Regional Director: Arnulfo M. Balane, CESO V

Development Team of the Module

Writer: Angelica T. Dagami

Language Editors: Rowena A. Caldosa, Jeff Bryan B. Caores, and
Thelma A. Presbitero
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Layout Artist: Eiderf John C. Go
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CLMD
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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-by-
step as you discover and understand the lesson prepared for you.

At the end of each module, you need to answer the test to self-check 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.

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For the learner:
Welcome to the Biotechnology 8 Self – Learning Module 1 on Tools of Genetic
Engineering!

The hand is one of the most symbolized parts of the human body. It is often used to
depict skill, action, and purpose. Through our hands, we may learn, create, and
accomplish. Hence, the hand in this learning resource signifies that you as a
learner is capable and empowered to successfully achieve the relevant
competencies and skills at your own pace and time. Your academic success lies in
your own hands!

This module was designed to provide you with fun and meaningful opportunities
for guided and independent learning at your own pace and time. You will be
enabled to process the contents of the learning resource while being an active
learner.

This module has the following parts and corresponding icons:

This will give you an idea of the skills or

competencies you are expected to learn in the
Explore module. A brief drill or review to help you link the
current lesson with the previous one. The new
lesson will also be introduced to you in various ways
such as a story, a song, a poem, a problem opener,
an activity, or a situation.
This section provides a brief discussion of the
lesson. This aims to help you discover and
Learn understand new concepts and skills.

This comprises activities for independent practice to

solidify your understanding and skills of the topic.
Engage You may check the answers to the exercises using
the Answer Key at the end of the module.
This includes questions or blank
sentences/paragraphs to be filled into the process
Apply what you learned from the lesson.

This is a task which aims to evaluate your level of

mastery in achieving the learning competency.
Assess

This contains answers to all activities in the module.

Answer Key

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 This contains the learner’s reflection. Learners are
encouraged to think about the lessons particularly
Reflect the parts that went well (they have understood) and
the parts that were weak (they have difficulty) and
write about it briefly. Learners can share their
thoughts and feeling about the lessons.

At the end of this module you will also find:

References This is a list of all sources used in developing
this module.

The following are some reminders in using this module:

1. Use the module with care. Do not put unnecessary mark/s on any part of
the module. Use a separate sheet of paper in answering the exercises.
2. Read the instructions carefully before doing each task.
3. Observe honesty and integrity in doing the tasks and checking your
answers.
4. Finish the task at hand before proceeding to the next.
5. Return this module to your teacher/facilitator once you are through with it.
If you encounter any difficulty in answering the tasks in this module, do not
hesitate to consult your teacher or facilitator. Always bear in mind that you are
not alone.

We hope that through this material, you will experience meaningful learning
and gain deep understanding of the relevant competencies. You can do it!

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5
 Explore

Introduction:

Hello! Congratulations for making it to this quarter! Are you ready for
another round of learning? Have you already watched the movie X-Men?
This science fiction movie depicts individuals with enhanced genetic
modification that give them special abilities.

In this module, you will be introduced to the basic concepts and

different tools commonly used in genetic engineering. This module also
discusses the different tools commonly used in genetic engineering.

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

Specifically, you are tasked to:

a. define genetic engineering;
b. state the history surrounding the progress of genetic engineering;
c. identify the tools commonly used in genetic engineering; and
d. appreciate the importance of the tools of genetic engineering.

Review

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 In the previous module, you learned about mutations. Let us try to
check if you could still recall the different types of mutations and different
genetic disorders caused by mutation.

Directions: Read the statement first then choose your answer from the box
below. Write your answers on a separate sheet of papers.

somatic mutation chromosomal alteration Marfan syndrome

point mutations frameshift mutations mutation
sickle cell anemia vitamin D-resistant hemophilia A
germline mutation

1. It is a mutation that occurs in gametes.

2. It is a mutation that occurs in other cells of the body.
3. It refers to mutations that change chromosome structure.
4. A change in a single nucleotide in DNA is called ______.
5. A deletion or insertion of one or more nucleotides that changes the reading frame
of the base sequence is called _________.
6. It results to defective protein in connective tissue.
7. It refers to the abnormal hemoglobin protein in red blood cells.
8. It is caused by lack of a substance needed for bones to absorb minerals.
9. It results from a reduced activity of a protein needed for blood clotting.
10. It refers to a change in DNA.

After performing this activity, rate yourself by comparing your answers with
the answer key. If you got a score of 8-10 then you are now ready to learn new
things from this module.

Learn

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Activity 1 SPOT THE DIFFERENCE
Directions: Observe the picture closely then answer the following questions.
Write your answers on a separate sheet of paper.

A B
A B (Wikimedia Commons, 2022)

Guide questions:
1. What do you observe in the pictures?
2. Which pair of tomato and cucumber is modified? Which is
not?
3. Which set of mice is modified? Which is not?
4. What is your basis of saying that a certain organism is
modified?
5. What do you think is the process or technique behind the
extraordinary feature of an organism?

What is Genetic Engineering?

In the previous lessons, you have learned about deoxyribonucleic acid

(DNA), a genetic material that carries the information needed to direct
protein synthesis and replication. Genetic engineering sometimes called
genetic modification, is a biotechnological process that helps modify or
improve the genetic traits of a particular organism. It is done by
manipulating genes, identifying the desired gene, and transferring it to
another organism. Genetically modified organism (GMO), GM crop, or
transgenic organism are the terms used to refer to the product of this
process (Navarette & Ochoco 2012).

History of Genetic Engineering

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 In order to understand the current state of genetic engineering, it is
important to understand the genome editing history. Some important events
include the discovery of the double helix, recombinant DNA (rDNA), human cancer
therapies, and more.

Here is a timeline of the discoveries and events in the history of genetic

modification to its present state:

● 1953- double helix (DNA) was discovered

● 1958 – DNA was made in the test tube for the first time
● 1962 – jellyfish protein turned into a tool to observe invisible cellular
processes
● 1967 – DNA ligase was discovered
● 1968 – restriction enzymes were discovered
● 1970 – type II Restriction Enzymes was successfully purified
● 1971 – gene splicing experiment paved the way for Recombinant DNA (rDNA)
● 1971 – type II restriction enzymes were used for mapping DNA
● 1972 – recombinant DNA was created
● 1975 – hybridoma technology revolutionized modern genetic diagnostics
● 1981 – the first transgenic animal was created
● 1982 – first genetically engineered human drug – synthetic insulin was made
● 1983 – Polymerase Chain Reaction (PCR) was developed
● 1986 – first recombinant vaccine for humans was approved
● 1988 – the first Bt Corn appeared in the fields
● 1993 – Clustered Regularly Interspaced Palindromic Repeats (CRISPR) was
discovered
● 1994 – a tomato engineered to stay ripe was brought to market
● 1996 – Dolly the sheep was cloned
● 1999 – history of genetic engineering in humans was made when the first
human chromosome was sequenced
● 2001 – the first gene targeted therapy was approved
● 2003 – sale of the Glo-fish - literally a fish that glows - as a pet for the home
● 2006 – the first preventative cancer vaccine was approved by FDA
● 2006 – the first induced pluripotent stem cells (iPSCs) was introduced
● 2010 – the world’s first synthetic life form, which technically means a living
organism that was entirely built rather than evolved or born.
● 2011 - Transcription Activator-like Effector Nucleases (TALENs) was
discovered
● 2012 – CRISPR genome engineering tool was discovered
● 2015 – a human embryo was edited with CRISPR
● 2018 – first human trials for CRISPR was approved

Tools used in Genetic Engineering

1. Enzymes

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A. Restriction Enzymes (Molecular Scissor)
● In the laboratory, restriction enzymes (or restriction
endonucleases) are used to cut DNA into smaller fragments. The
cuts are always made at specific nucleotide sequences. Different
restriction enzymes recognize and cut different DNA sequences.
● Like all enzymes, a restriction enzyme works by shape-to-shape
matching. When it comes into contact with a DNA sequence
with a shape that matches a part of the enzyme, called
the recognition site, it wraps around the DNA and causes a
break in both strands of the DNA molecule.
● Each restriction enzyme recognizes a different and
specific recognition site, or DNA sequence. Recognition sites
are usually only short - 4-8 nucleotides.
● The discovery of restriction endonucleases has been essential to
protein engineering. Hundreds of different restriction enzymes,
capable of cutting DNA at a distinct site have been isolated from
many different strains of bacteria. DNA cut with a restriction
enzyme produces many smaller fragments of varying sizes.
These can be separated using gel electrophoresis or
chromatography.

(ScienceLearningHub – Pokapū Akoranga Pūtaiao 2007)

Figure 2. A restriction enzyme

breaking both strands of DNA

B. DNA Ligase

● In DNA replication, ligase’s job is to join together fragments of

newly synthesized DNA to form a seamless strand. The ligases
used in DNA cloning do basically the same thing. If two pieces of
DNA have matching ends, DNA ligase can join them together to
make an unbroken molecule.
● In molecular biology, DNA ligase can be used to insert genes of
interest into plasmid vectors or to create fusion genes by joining

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 one gene onto another. This process is called ligation (literally
“tying a knot”).

C. Alkaline phosphatases
● Phosphatases are a group of enzymes which remove a
phosphate from a variety of substrates like DNA, RNA, and
proteins. Phosphatases which act in basic buffers with pH 8 or
9 are called alkaline phosphatases.

D. Polymerases
The groups of enzymes that catalyze the synthesis of nucleic acid
molecules are collectively referred to as polymerases. It is customary
to use the name of the nucleic acid template on which the polymerase
acts. The three important polymerases are given below.
▪ DNA-dependent DNA polymerase that replicates DNA from
DNA.
▪ RNA-dependent DNA polymerase (reverse transcriptase) that
transcribes DNA from RNA.
▪ DNA-dependent RNA polymerase that transcribes RNA from
DNA

2. Vectors
In molecular biology, a vector is a DNA molecule used as a vehicle to
transfer foreign genetic material into another cell.
Four major types of vectors:
A. Plasmids are small, circular pieces of DNA that are not part of the
bacterial genome but are capable of self-replication. It is used as
vectors to transport genes between microorganisms. Once the gene of
interest has been amplified with PCR, the gene and plasmid are cut by
restriction enzymes and ligated together. The resulting combination is
known as Recombinant DNA.

B. Viral Vectors are used for the delivery of genetic material into
cells. Because viruses have a natural ability to efficiently deliver their
genome into host cells, they are an ideal tool for gene transfer and are
often used by molecular biologists to deliver therapeutic genes.

C. Cosmids are hybrids between plasmid and phage λ (Lambda)

vectors. They are designed to clone large fragments of DNA and to
grow their DNA as a virus or as a plasmid.

D. Artificial Chromosomes is a type of cloning vector that has some

features of true chromosomes and is used to clone relatively large
fragments of DNA. 

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 Examples:
Bacterial artificial chromosomes (BACs) - are based on the F
(fertility) plasmid found naturally in E. coli bacteria
Yeast artificial chromosomes (YACs) - are linear vectors derived
from a circular plasmid found naturally in baker's yeast
(Saccharomyces cerevisiae)

3. Polymerase Chain Reaction (PCR)

● Sometimes called "molecular photocopying," the polymerase
chain reaction (PCR) is a fast and inexpensive technique used to
amplify and copy small segments of DNA. Because significant
amounts of a sample of DNA are necessary for molecular and
genetic analyses, studies of isolated pieces of DNA are nearly
impossible without PCR amplification.
● Usually publicized as one of the most important scientific
advances in molecular biology, PCR revolutionized the study of
DNA to such an extent that its creator, Kary B. Mullis, was
awarded the Nobel Prize for Chemistry in 1993.
● Once amplified, the DNA produced by PCR can be used in many
different laboratory procedures. For example, most mapping
techniques in the Human Genome Project (HGP) relied on PCR.
● PCR is also valuable in a number of laboratory and clinical
techniques, including DNA fingerprinting, detection of bacteria
or viruses (particularly AIDS), and diagnosis of genetic
disorders.
● To amplify a segment of DNA using PCR, the sample is first
heated so the DNA denatures, or separates into two pieces of
single-stranded DNA. Next, an enzyme called "Taq polymerase"
synthesizes and builds two new strands of DNA, using the
original strands as templates. This process results in the
duplication of the original DNA, with each of the new molecules
containing one old and one new strand of DNA. Then each of
these strands can be used to create two new copies, and so on.
The cycle of denaturing and synthesizing new DNA is repeated
as many as 30 or 40 times, leading to more than one billion
exact copies of the original DNA segment.
● The entire cycling process of PCR is automated and can be
completed in just a few hours. It is directed by a machine called
a thermocycler, which is programmed to alter the temperature
of the reaction every few minutes to allow DNA denaturing and
synthesis.

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 (National Human Genome Research Institute 2020)

Figure 1. Polymerase Chain Reaction process

4. Gel Electrophoresis
● Gel electrophoresis is a technique usually employed in
laboratories to separate charged molecules like deoxyribonucleic
acid, RNA, and proteins per size. Charged molecules move
through a gel once an electrical current is passed across it. The
movement of molecules is termed migration. Molecules migrate
towards the other charge. Thus, molecules like DNA and RNA
that are negatively charged are forced towards the positive end.
The molecules travel through the pores in the gel at a speed that
is inversely related to their lengths. This means that a smaller
molecule will travel a lot quicker through the gel than will a
larger DNA molecule. As a result, the molecules area unit are
separated by size (yourgenome 2016).
●

Figure 3. Illustration of DNA electrophoresis

equipment used to separate DNA fragments
by size. A gel sits within a tank of the buffer.
The DNA samples are placed in wells at one
end of the gel and an electrical current
passed across the gel. The negatively-
charged DNA moves towards the positive
electrode.
Image credit: Genome Research Limited
(yourgenome 2021)
5. Prokaryotic host

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 ● The bacterium, 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. As the bacteria multiply, their plasmids
(along with foreign DNA) also multiply to produce millions of
copies, referred to as a colony or in 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.

6. Eukaryotic host
● Eukaryotic organisms 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.
7. Transformation/Transduction
● Transformation is the process of transferring genetic material
in a vector, such as a plasmid, into host cells. The host cells are
exposed to an environmental change, such as electroporation,
which makes them “competent” or temporarily permeable to the
vector. The larger the plasmid, the lower the efficiency with
which it is taken up by cells.
● Transduction is a method in which larger DNA segments are
more easily cloned using bacteriophage, retrovirus, or other
viral vectors or cosmids. Phage or viral vectors are often used in
regenerative medicine but may cause the insertion of DNA in
parts of our chromosomes where we don’t want it, causing
complications and even cancer.

Notes to the Teacher

Engage
The teacher may modify this module. The teacher may give
additional activities and performance tasks to the learners.

Activity 1

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Directions: Write the missing letters to form the word in each item. Then
use the letters that correspond to the given numbers to discover the
“keyword”. Write your answer on a separate sheet of paper.

Keyword: __ __ __ __ __ __ __ __ __ __
1 2 3 4 5 6 7 8 9 10

Words to Complete Clues

1. l __ g __ __ __ __ n joining one gene to another
1
2. __ e __ e __ __ __ t __ __ __ h __ r __ s __ __ method used to separate
2 mixtures of DNA, RNA and
proteins

3. y __ __ s __ eukaryotic organism used in

3 brewing and baking industry
4. __ __ c __ m __ i __ __ __ t D __ __ resulting product of
4 combining DNA from
different sources

5. p __ __ __ m __ r __ __ __ s group of enzymes that

5 catalyse the synthesis of
nucleic acid molecules

6. l __ __ a __ e joins together two pieces of

6 7 DNA with matching ends

7. p __ __ m __ __ s short DNA sequences

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8. __ r __ __ s __ __ r __ __ t __ __ n transferring genetic material
8 9 in a vector into host cells

9. __ o __ m __ d __ hybrids between plasmid and
9 phage λ vectors
10. __ l __ n __ refers to a mass of cells that
10 results from the
multiplication of a single cell

Activity 2
Directions: Identify which tool of genetic engineering is being described.
Rearrange the jumbled letters in each box to help you out.

NLIEKLAA HSHAOPPSSTAE CTROEV ASGILE

MROLYEPSASE SIDSOMC
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_______1. It is a group of enzymes which remove a phosphate from a variety
of substrates like DNA, RNA and proteins.
_______2. It refers to a DNA molecule used as a vehicle to transfer foreign
genetic material into another cell.
_______3. It is used to insert genes of interest into plasmid vectors or to
create fusion genes by joining one gene onto another.
_______4. It refers to the groups of enzymes that catalyze the synthesis of
nucleic acid molecules.
_______5. These are designed to clone large fragments of DNA and to grow
their DNA as a virus or as a plasmid.

Apply

Activity 1
Essay No. 1

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Directions: In at least five sentences, define genetic engineering using the
given keywords. You can cite some advantages and disadvantages of genetic
engineering in your essay.
Keywords:
Modify Gene Transfer
Transgenic Organism

Essay No. 2
Directions: Read the statement below then answer the corresponding
questions. Be guided with the given rubric in constructing your essay.
When the COVID-19 pandemic began, Reverse-transcriptase
Polymerase Chain Reaction (RT-PCR) tests were the first to be developed and
widely deployed, and remained the primary tool used for diagnosis. What is
the role of this tool in managing the spread of COVID-19? What is its impact
to the society? How important is this RT-PCR test?
Rubric for Scoring
Bases 5 4 3 2
Ideas All ideas are Most ideas are Some ideas are Ideas has no
related to the related to the topic really good parts clear sense
topic with with good details and some aren’t of purpose
excellent details there yet
Organization Easy to read, Well organized Some smooth Information
has smooth with an interesting parts are is not
transitions and hook, good included while relevant; no
awesome transitions, and a others need beginning
conclusion clear conclusion work. nor end
Conventions Punctuation Commit few minor Commit several Some errors
and grammar errors in spelling, errors in spelling, confuse the
are correct. The punctuation, and punctuation, and reader
writing is free grammar grammar
from spelling
errors

Assess

I. Multiple Choice. Choose the letter of the best answer. Write your
answers on a separate sheet of paper.
1. It is the process of altering DNA in an organism’s genome.
A. transduction
B. transformation
C. DNA replication

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 D. genetic engineering

2. Which of the following is NOT a function of DNA ligase?

A. to amplify DNA sequences
B. to insert genes of interest into plasmid vectors
C. to join together two matching ends of DNA to make an unbroken
molecule
D. to join together fragments of newly synthesized DNA to form a
seamless strand

3. In 1971, what paved the way for recombinant DNA?

A. the discovery of CRISPR
B. the gene splicing experiment
C. the discovery of restriction enzymes
D. the development of polymerase chain reaction

4. What breakthrough happened in 1996?

A. the discovery of TALENs
B. the discovery of CRISPR
C. the cloning of Dolly the Sheep
D. the creation of first genetically engineered human drug

5. Why are genetic engineering tools important?

A. It aids in the creation of transgenic organisms.
B. It allows the function of specific genes to be studied.
C. Through these tools, drugs, vaccines and other products have been
harvested from organisms engineered to produce them.
D. All of the above.

II. Table Completion

Directions: Copy the table in your answer sheet. Complete it by giving the
description for each genetic engineering tool.

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 Tools Used in Genetic Description
Engineering
1. Restriction Enzymes
2. Vectors
3. Polymerase Chain Reaction
4. Gel Electrophoresis
5. Eukaryotic Host

Reflect

Share your thoughts and feelings about the module by

answering the following questions. Write your answer on a separate sheet of
paper.
1. Which part of the lesson did you find easy?

___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
___________________________.
2. Which part of the lesson did you find challenging? What did you do
to deal with it?

___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
___________________________.

Answer Key

Review Learn Engage

Germline Activity 1 Activity 2
mutation
Somatic 1. It turns brown Ligation
mutation 14 Gel
Chromosomal 2. The first apple electrophoresis
alteration turns brown after slicing Yeast
Point Mutation while the other apple did Recombinant
Frameshift not DNA
mutation Polymerases
 Engage Assessment
Activity 3 D
A
1. Alkaline Phosphatases B
2. Vector C
3. Ligase D
4. Polymerases
5. Cosmids

References

Books
Navarette, Bonifacio V. and Ochoco, Sheila Marie A. (2012) Discover Science
Biology, Diwa Learning Systems Inc.

Website

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Biesecker, L. (2020). National Human Genome Institute.
https://www.genome.gov/sites/default/files/inline-images/PCR_Fact-
sheet2020.jpg
Biesecker, L. (2020). National Human Genome Institute.
https://www.genome.gov/genetics-glossary/Polymerase-Chain-Reaction
Brown et.al. (2000) Artificial Chromosomes: Ideal Vectors?
https://www.cell.com/trends/biotechnology/fulltext/S0167-7799(00)01438-
4#:~:text=Artificial%20chromosomes%20are%20DNA%20molecules,many
%20aspects%20of%20yeast%20genetics.
Commons.wikimedia.org. 2022. File:GFP Mice 01.jpg - Wikimedia Commons. [online]
Available at: <https://commons.wikimedia.org/wiki/File:GFP_Mice_01.jpg>
[Accessed 15 June 2022]. Creative Commons Attribution 2.0 Generic
"File:Organic And Gmos Tomatoes & Cucumbers.Jpg - Wikimedia Commons".
2022. Commons.Wikimedia.Org.
https://commons.wikimedia.org/wiki/File:Organic_and_GMOs_tomatoes_
%26_cucumbers.jpg. Creative Commons Attribution-Share Alike 4.0 International
Khan Academy (2021) Restriction Enymes and DNA Ligase.
https://www.khanacademy.org/science/biology/biotech-dna-technology/dna-
cloning-tutorial/a/restriction-enzymes-dna-ligase
Minchin, S. (2021). Facts, Genetics. Explore Biotech.
https://explorebiotech.com/10-tools-for-genetic-engineering/
National Human Genome Research Institute. (2020).
"https://www.genome.gov/about-genomics/fact-sheets/Polymerase-Chain-
Reaction-Fact-Sheet. Public Domain
Nature Education. (2014) https://www.nature.com/scitable/definition/gel-
electrophoresis-286/
Science Learning Hub (2007, November 20). Restriction Enzymes
https://www.sciencelearn.org.nz/resources/2035-restriction-enzymes
Synthego. (2021) History of Genetic Engineering and the Rise of Genome Editing
Tools https://www.synthego.com/learn/genome-engineering-history
Udugama et.al. (2020). Diagnosing COVID-19: The Disease and Tools for Detection
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7144809/

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