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Biotechnology
Quarter 3– Module 4
Mapping the Genome
Biotechnology – Grade 8
Alternative Delivery Mode
Quarter 3 – Module 4: Mapping the Genome
First Edition, 2021

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E-mail address: [email protected]

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 8

Biotechnology
Quarter 3– Module 4
Mapping the Genome
4
Introductory Message
This Self-Learning Module (SLM) is prepared so that you, 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.

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 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 Teachers 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 exercise and tests. 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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 What I Need to Know

This module encourages you to discuss how the Genetic Materials are
manipulated. Various activities are provided for you to strengthen your knowledge and
skills regarding the topic.

At the end of this module, you are expected to:

• identify Human Genome Project;
• trace the historical events that paved way to the development of Human
Genome Project;
• describe gene mapping, gene identification and DNA Sequencing as the
techniques involved in the Human Genome Project; and
• appreciate the importance of Human Genome Project in the field of Sciences.

What I Know

A. Directions: Choose the letter of the best answer. Write the letter of your
choice on a separate sheet of paper.

1. Approximately, how many genes do the human genome have?

A. 20,000- 25,000 C. 35,000- 40,000
B. 30,000- 35,000 D. 35,000- 50,000
2. How many percent of human genome actually encodes functional proteins?
A. 1% B. 2% C. 5% D. 35%
3. It is a continuous stretch of codons that begins with a start codon( usually ATG) and
ends with a stop codon (TAG)
A. MPs B. ORF C. RFLPs D. VNTRs
4. What is the ultimate goal of Human Genome Project?
A. Addresses ethical, legal and social issues (ELSI) associated with the project.
B. Deciphers the function of each of the genes estimated to be present in the
human genome.
C. Develops faster, more efficient technologies for data analysis.
D. Stores DNA information in databases.
5. Which of the following best describes DNA sequencing?
A. Determining the exact order of the base pairs in a segment of DNA.
B. Determining the exact order of the phosphate in a DNA.
C. Determining the exact location of genes on the chromosome.
D. Determining the exact location of phosphate in a DNA.

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B. Directions: Write TRUE if the statement is correct and FALSE if it is incorrect.

____1. Fredrick Sanger developed a technique for DNA sequencing, known as the
Sanger’s method of DNA sequencing.
____2. In 1990, HGP was officially launched with James Watson as its Project
Director.
____3. Markers are any inherited physical or molecular characteristics that are the
same among individuals of a population (polymorphic).
____4. Robert Sanger at UCSC proposed the idea of sequencing the human
genome.
____5. Restriction Fragment Length Polymorphisms (RFLPs) reflects sequence
differences in DNA sites which cleaved by restriction enzymes.
____6. A genetic map shows the relative locations of specific markers on the
chromosomes.
____7. In 1995, First Human Gene map was published. Yeast genome was sequenced.
HGP’s mouse genetic mapping goal was achieved.
____8. Double stranded DNA fragment to be sequenced is first labeled by attaching
a radioactive phosphorous group to the 5’ end of each strand.
____9. Improvements in diagnostic and therapeutic applications in the field of medicine
are the application of the Human Genome Project.
____10. DNA Polymerase incorporates deoxynucleotide triphosphates (dNTPs)
complementary to the template strand and extend to the DNA Chain with five
prime to three prime direction.

What’s In

Directions: A set of applications are expressed in word/phrase around DNA

Fingerprinting. Draw an arrow from the word/phrase pointing toward
the DNA Fingerprinting if the word/phrase is related to the DNA
Fingerprinting.

Development of Cures for Inherited Disorders

Paternity and Maternity test Phylogenetic Analysis

DNA
Breeding Program FINGER- Forensic Science
PRINTING
Gene Mapping Personal Identification

Diagnosis of Inherited Disorders

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 What’s New

Word Loop

Directions:
1. Locate the five (5) hidden words in the grid below. The words are written vertically,
horizontally, or diagonally.
2. After determining the five hidden words, there are unused letters left in the grid .
3. Arrange the unused letters to form one (1) word that will describe the five hidden
words.
4. Write your answer on a separate sheet of paper.

T G E N O M E C E O G

T E R M I N A T I O N

E A N U E M J O P N M

N U C L E O T I D E S

T S E Q U E N C I N G

E H R M A P P I N G H

Hidden words:_______________________________________________________

Notes to the Teacher

The activities in this module are arrange from simple to complex to
help the learner gradually master the desired learning competencies. Give
him/her the needed support and guidance so that he/she will be able to
perform the tasks to prepare him/her later on in learning Mapping the
Genome.

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 What is It

Mapping the Genome

Human Genome Project (HGP)

The Human Genome Project (HGP) was an international, collaborative research
program that focused on the complete mapping and understanding of all the genes of
human beings. Genes support the information for making all of the proteins required by
the body for development and maintenance. Genes made up around 35,000 – 50,000
genes code for the functional proteins in the body. Our genes are collectively known as
genome which is the hereditary material of all multi-cellular organisms in the
famous double helix of deoxyribonucleic acid DNA. “Human genome” involved
sequencing the genomes of a small number of individuals and then constructing these
together to get a complete sequence for each chromosome.
The Human Genome Project aimed to identify and map all the ~35,000 – 50,000
genes (approximate) in the human DNA from a physical and functional standpoint. It
aimed to determine the sequences of the three billion chemical base pairs that make
up the human DNA, as well as to sequence the genomes of other organisms that
are significant in medical research such as mouse, drosophila etc. The ultimate goal of
the Human Genome Project was to decipher the function of each genes estimated to be
present in the human genome.
The Project has the following goals: 1. to develop faster, more efficient technologies
for data analysis; 2. to store DNA information in databases; and 3. to allow the private
sector access to the information and technologies that arise from this project. The Human
Genome Project wants to address ethical, legal and social issues (ELSI) associated with
the project.
The Human Genome Project (HGP), which operated from 1990 to 2003, provided
researchers with basic information about the genetic content of the human organism,
opening new avenues of discovery in fields such as cancer research.

How does the Human Genome Project develop?

Timeline Development of Human Genome Project

 1970- The Sanger’s Method of DNA Sequencing was developed by Fredrick Sanger.

 1985- Robert Sinsheimer at UCSC proposed the idea of sequencing the human
genome

 1986- The Human Genome Project was came forward to fund by the U.S.
Department of Energy and the National Institute of Health. .

 1989- U.K.’s medical research council (MRC) joined the Human Genome Project.

 1990- HGP was officially launched with James Watson as its Project Director.

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 The first gene to be mapped was BRCA1, which is the gene for breast cancer.

 1993- First fifth (5th)year plan for HGP was published. Sanger Institute (UK) joins HGP.

 1994- HGP’s Human genetic mapping goal was achieved.

 1995- Genetic privacy act was passed. First bacterial genome was sequenced
(Hemophilus influenzae).

 1996- First Human Gene map was published. Yeast genome was sequenced. HGP’s
mouse genetic mapping goal was achieved.

 1997- The National Institutes of Health (NIH) becomes National Human Genome
Research Institute (NHGRI), E.coli genome sequenced. And Genoscope,
French National Genome Sequencing Centre was established.

 1998- Second fifth (5th) year plan for was published. Japan’s RIKEN Genomic Services
Centre was established. Genome of the roundworm Caenorhabditis elegans
was sequenced. SNP sequencing was initiated. In Beijing and Shanghai, the
Chinese National Human Genome Centres were established.

 1999- Sequencing of human chromosome 22 was completed and published in “The

Nature”.

 2000- Working draft of human genome completed. U.S. President Clinton and UK’s
PM Blair supported free access to genome information. Genomes of D.
melanogaster and A. Thaliana were sequenced and published in “The Nature”.
In the same year Jim Kent, a PhD scholar in the University of California Santa
Cruz ( UCSC), developed a software, GigAssembler, that allowed the publicly
funded Human Genome Project to gather and publish the human genome
sequence.

 2001- Working draft of human genome sequence was published in “The Nature and
Science”.

 2002- Working draft of mouse genome sequence was completed and published.

 2003- Finished version of genome sequence was completed. Human Genome Project
ended with all the goals achieved.

The Human Genome Project used different techniques to determine the sequence
of human genome and other organisms. These are the techniques involved in Human
Genome Project.

 Determining the human genome first involves genome mapping, or characterizing the
chromosomes.

 The next step is DNA sequencing, or determining the order of DNA bases on a
chromosome.

 The process of identifying the boundaries between genes and other features in a raw of
DNA sequence is called Gene identification.

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 Gene Mapping

Gene mapping is the procedure of identifying the location of genes on each

chromosome. The study of entire genomes, including the complete set of genes, their
nucleotide sequence and organization, and their interactions within a species and with
other species is called genomics.

Types of Gene Maps:

1. Genetic maps are illustration that list genes and their locations on a
chromosome. They provide the big picture (similar to a map of intensive highways)
and use genetic markers (similar to landmarks).
2. Physical maps present the intimate details of smaller regions of the
chromosomes (similar to a detailed road map). They are the illustrations of
the physical distance, in nucleotides, between genes or genetic markers.

Both genetic maps and physical maps are collections of genetic markers and
gene loci, and they are required to build a complete picture of the genome. The nature
of all genome mapping is to set the collection of molecular markers onto their specific
positions on the genome. It is easier for researchers to study individual genes if they
have a complete map of the genome. Researchers can easily identify human disease
-causing genes related to illnesses like cancer, heart disease, and cystic fibrosis using the
human genome map.

Gene mapping can be used in a different applications, such as using live microbes
to clean up pollutants or even prevent pollution. Research including plant genome
mapping may cause higher crop yields or developing plants that better adapt to global
climate change.
Genetic Map

Cytogenic Map

Physical Map

DNA Sequence
Figure 1. Gene Maps

Genetic marker is a gene or sequence on a chromosome that co-segregates

with a specific trait.

Genetic markers used in generating genetic maps.

1. Restriction Fragment Length Polymorphisms (RFLPs) are detected when the
DNA of an individual is cut with a restriction endonuclease that recognizes specific
sequences in the DNA to generate a set of DNA fragments, then examined by
gel electrophoresis.
2. Variable Number of Tandem Repeats (VNTRs) are repeated sets of nucleotides
present in the non-coding regions of DNA.

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 3. Microsatellite Polymorphisms (MPs) are as same as VNTRs, however the
repeat unit is very small.
4. Single Nucleotide Polymorphisms (SNPs) are variations in a single nucleotide.
Physical maps provide detail of the particular physical distance between genetic
markers, also including the number of nucleotides. Physical maps can be created using
the following methods.
Three Methods Used to Create Physical Maps
1. Cytogenetic mapping. It uses information gathered by microscopic analysis of
stained sections of the chromosome. It is possible to find the approximate
distance between genetic markers using cytogenetic mapping, but not the exact
distance ( number of base pairs).
2. Radiation hybrid mapping. It uses radiation, like x-rays, to cut the DNA into
fragments. It overcomes the limitation of genetic mapping and is not suffering
from increased recombination frequency.
3. Sequence mapping. This is attained from DNA sequencing technology that
permits the creation of detailed physical maps with distances measured in terms of
the number of base pairs.

How do researchers create a genetic map?

Researchers start a genetic map by collecting samples of blood, saliva, or tissue
from family members that carry a prominent disease or trait and family members that do
not. The most common sample utilized in gene mapping, especially in personal genomic
tests is saliva. Scientists then isolate DNA from the samples and closely examine it,
finding the unique patterns within the DNA of the family members who do carry the
disease and with those who don't carry the disease. These unique molecular patterns
within the DNA are mentioned to as polymorphisms, or markers. After making gene
mapping researcher can use it to identify the genes.

Gene Identification

Gene identification is also referred to as “gene prediction or gene finding”. It refers

to the method of identifying the regions of genomic DNA that encode genes. This
includes protein -coding genes also RNA genes, but can also include prediction of
other functional elements like regulatory regions. It is one of the primary and most
significant step in understanding the genome of a species once it has
been sequenced.Target genes are often identified through searching online databases for
long stretches of DNA that would potentially code for protein.

Open Reading Frames (ORFs)

Open reading frame is a part of a reading frame that has the ability to be translated.
It is a continuous stretch of codons that begins with a start codon( usually ATG) and ends
with a stop codon (TAG,TGA or TAA). Typically, it consists of at least 100 codons
equivalent to 300 nucleotides. Any particular stretch of DNA double stranded and
either strand will have six reading frame that could potentially code for a functional
protein. While employing an mRNA, it is translated in codons (triplets of bases),
meaning there are three potential reading frames for a given DNA sequence.
Open reading frames can be identified in a given DNA sequence using the following
ways.
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 1. Locate a sequence corresponding to a start codon (ATG) in order to determine
the reading frame.
2. Read this sequence in base triplets until a stop codon is reached. (TAG,TGA or
TAA)
3. The longer the sequence, the more significant the likelihood that the sequence
corresponds to an open reading frame.

Let us take a look at the example of identification of an open reading frames (ORFs)

ATG ACA CGA TAT GAG ATA TGC ATA GAA AGC GAA TAT AGA TAG
Frame 1

A TGA CAC GAT ATG AGA TAT GCA TAG AAA GCG AAT ATA GAT AG
Frame 2
AT GAC ACG ATA TGA GAT ATG CAT AGA AAG CGA ATA T AG ATA G
Frame 3

Identify the three open reading frames ( ORFs).

ATGCAATGGGGAAATGTTACCAGGTCCGAACTTATTGAGGTAAGACAGATTTAA

Common Methods Used in Gene Identification

1. Empirical or Homology Method-it is gene finding system, the target genome is
searched for sequence that are similar to extrinsic evidence in the form of
known expressed sequence tags, messenger RNA (mRNA), protein products,
and homologous or orthologous sequences.
2. Ab Initio method-it is an intrinsic method on gene content and signal
detection, may be characterized as gene prediction, since extrinsic evidence is
required to absolutely establish a functional putative gene.

DNA Sequencing
DNA sequencing is a method of finding the sequence of nucleotides within DNA
molecule. Every organism’s DNA consists of a specific sequence of nucleotides.
DNA sequence may help the scientists to compare the DNA between organisms, and
which can help show how the organisms are related.
By sequencing a stretch of DNA, it will be possible to understand the order of the
four nucleotide bases - adenine, guanine, cytosine and thymine - found within the
nucleic acid molecule.
There are two main types of DNA sequencing - the older, classical chain termination
method also known as Sanger Method and the newer method that can process a large
number of DNA molecules quickly are called High -Throughput Sequencing (HTS) or Next
- Generation Sequencing (NGS) method.

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Chain Termination Method (Sanger Sequencing Method)
Sanger sequencing was developed by Frederick Sanger and his colleagues at
University of Cambridge in 1977. It is a DNA sequencing method in which target DNA
template strand is denatured and annealed to anoligonucleotide primer, which is then
extended by DNA polymerase using a mixture of deoxynucleotides triphosphates (normal
dNTPs) and chain-terminating dideoxynucleotide triphosphates (ddNTPs).
Sanger sequencing method is the original DNA sequencing method which
served as basis on automated computer sequencing. It involves in vitro DNA
synthesis and is based on principle of biochemistry of DNA replication.

Figure 2. Basic requirements for in vitro DNA synthesis

What are the basic requirements for in vitro DNA synthesis?

1. DNA template strand. This strand will provide complement three bases for
DNA synthesis for new strand.
2. Primer. It is a short nucleic acid sequence complementary to the sequence at
the three primer end of the template strand. It serves as the stopping point for
new strand synthesis.
3. Deoxynucleotide triphosphates (dNTPs). These are the components of DNA,
which contain the phosphate, sugar, and organic base.
4. DNA Polymerase. It is used to catalyze the DNA synthesis reaction. It
incorporates deoxynucleotides triphosphates (dNTPs) complementary to the
template strand and extends to the DNA Chain with five prime to three
prime direction.

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 Why primer is essential requirement in DNA
synthesis?
Primer is essential for the DNA synthesis
because DNA Polymerase cannot catalyze the
synthesis reaction on its own, it requires three prime
hydroxyl group to form Phosphodiester bond with
the incoming deoxynucleotide triphosphate (dNTP)
and this initial three prime hydroxyl group is
provided by the primer. Once DNA synthesis
initiated, each deoxynucleotide incorporated in the
growing DNA chain has a hydroxyl group of the
three prime position of the deoxyribose
molecule and thus DNA Polymerase keeps Figure 3. Phosphodiester bond
on elongating the chain.

Sanger DNA sequencing technique makes use of modified deoxynucleotides

known as Dideoxynucleotide Triphosphates (dDNTPs). Here are the basic chemical
structure of Deoxynucleotide Triphosphates (dNTPs) and Dideoxynucleotide
Triphosphates (ddNTPs).

As you can see in figure 4. Deoxynucleotide

Triphosphates (dNTPs), the three prime position of
sugar hydroxyl group (OH) is present. This is the
three prime hydroxyl group which is participated in
phosphodiester bond formation during DNA
synthesis.
Figure 4. Deoxynucleotide Triphosphates (dNTPs)

In figure 5. Dideoxynucleotide Triphosphates

the hydroxyl group (OH) is absent at the three
prime position of the sugar instead there is a
three prime hydrogen in dideoxynucleotide
triphosphate.

Figure 5. Dideoxynucleotide Triphosphates (dDNTPs)

What will happen if dideoxynucleotide triphosphates is added to a DNA synthesis

reaction?
DNA synthesis will terminate with the incorporation of this dideoxynucleotide
triphosphates (ddNTPs), because there is no prime hydroxyl group for the further
extension of DNA chain. For this reason, the dideoxynucleotide triphosphates are called
chain termination nucleotides. Sanger technique is also known as chain termination
method or dideoxy DNA Sequencing.

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Three Steps of Sanger Sequencing Method

1. DNA Extraction: using any of the DNA extraction protocols

DNA extraction and purification are the starting steps of chain termination.
DNA extraction are often achieved using the proteinase K method or the phenol
-chloroform DNA extraction method. The ready to use silica-column based kit can also
be utilized as another method. The main goal of any DNA extraction method is to
achieve the purity of the DNA.

2. PCR Amplification: using the flanking primers, dNTPs, ddNTPs, DNA

polymerase and PCR buffer.

Steps in PCR Amplification

A. Place the single strand of DNA in the PCR machine to provide many strands
of DNA and these can be used for DNA synthesis. Designing four different
reactions can be performed in PCR amplification.
B. Place the copies of DNA template strand in every reaction tube. Each
reaction tube contains the equivalent amount of the PCR reagents but in
each tube, and with additional ddNTPs.

“A” reaction “C” reaction “G” reaction “T” reaction

tube tube tube tube
contains contains contains contains
ddATP ddCTP ddGTP ddTTP

Figure 6. Four Reaction tubes

Sanger Sequencing method consists of four separate reaction tubes that run
parallel. We will label each reaction tubes A, C, G and T. Each reaction tubes has
different small amount of dideoxynucleotide triphosphates (ddNTPs). For our illustration
ddATPs is added in the “A” reaction tube, ddCTPs in “C” reaction tube, ddGTPs “G”
reaction tube and ddTTPs in “T” reaction tube. Each reaction tubes contains similar
components.

Common Components in each Reaction Tubes

1. DNA Template strand (many copies are used in each reaction)
3’ TACGTGAACTAG 5’
2. DNA primer (many copies of primer are used in Sanger radiolabeled as detection
purpose) . 5’ 3’
3. DNA polymerase
4. Deoxynucleotide Triphosphates - (dATPs, dCTPs, dGTPs, and dTTPs are the
four dNTPs or deoxynucleotide triphosphates).

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 C. The flanking primers are primers that bind to the region near the sequence
of interest or the sequence which will be read.
D. DNA polymerase adds the dNTPs to the DNA strand.

DNA polymerase expands the growing DNA strand by the addition of the
dNTPs. Interestingly, once it adds the ddNTPs instead of dNTPs the chain
expansion is stopped or terminated.

The four (4) different tubes for four (4) different ddNTPs complete the
termination process. For example, in the ddATPs tube, it terminates the chain at all
the positions where the dATPs are going to bind. DNA synthesis will not terminate
every time but DNA polymerase will occasionally insert a ddNTPs instead of a
dNTPs into growing DNA strand because the incorporated ddNTPs lacks three prime
hydroxyl group it cannot form a bond with another nucleotide and DNA synthesis will
terminate thus in each case researchers will get partially replicated fragments, since
small amounts of ddNTPs are included in each reaction

Let us understand this for the “A” reaction tube , this our DNA template strand
and primer. ddATPs is present in lower amount, and will be incorporated occasionally
wherever normal dATPs is to be incorporated complementary to thymine residue and
each time a ddATPs has incorporated, the DNA synthesis terminates. As you can see
there are thymine residues in the template strand, complementary to these thymine
residues, ddATPs can be incorporated in the new strand at the end of this reaction there
will be three partially replicated DNA fragments.
.
5’ 3’
3’ TACGTGAACTAG 5’
“A” reaction
tube 5’ A 3’
contains 5’ ATGCA 3’
ddATP 5’ ATGCACTTGA 3’

Figure 7. DNA fragments in “A” reaction tubes

Similarly three partial replication products will be produced in “C” reaction tube
where ddCTPs will be incorporated occasionally complementary to guanine residue.

5’ 3’
3’ TACGTGAACTAG 5’
“C” reaction
tube 5’ ATGC 3’
contains
5’ ATGCAC 3’
ddCTP
5’ ATGCACTTGATC 3’

Figure 8. DNA fragments in “C” reaction tubes

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 In the “G” reaction tube two of the partial replication products are produced. Where
ddGTPs will be incorporated occasionally complementary to cytosine residue.
5’ 3’
3’ TACGTGAACTAG 5’
“G” reaction
5’ ATG 3’
tube
5’ ATGCACTTG3’
contains
ddGTP
Figure 9. DNA fragments in “G” reaction tubes

In the “T” reaction tube four of the partial replication products are produced. Where
ddTTPs will be incorporated occasionally complementary to adenine residue
5’ 3’
3’ TACGTGAACTAG 5’
“T” reaction
5’ AT 3’
tube
5’ ATGCACT 3’
contains
ddTTP 5’ ATGCACTT 3’
5’ ATGCACTTGAT 3’

Figure 10. DNA fragments in “T” reaction tubes

3. Identification of the amplified fragments: using autoradiography, PAGE, or

capillary gel electrophoresis.

Steps in Identification of the Amplified Fragments

A. The polyacrylamide gel electrophoresis are loaded by amplified PCR DNA
fragments. Based on the size of the fragments, the DNA fragments migrate
into the gel. The smaller fragments run faster going through the positive
charge than larger fragments.

B. The amplified DNA fragments are further denatured by heat before the PAGE
run. Depending upon the types of labeling the gel is then examined under UV
light or X-ray film. Sanger radio labeled the primers in each reaction mixture
autoradiograph of the gel was obtained.
C. The last step simply involves reading the gel to determine the sequence of the
input DNA. Since DNA polymerase only synthesizes DNA in the 5’ to 3’ direction
starting at a provided primer, each terminal ddNTPs will correspond to a specific
nucleotide in the original sequence (e.g., the shortest fragment must terminate
at the first nucleotide from the 5’end, the second-shortest fragment must terminate
at the second nucleotide from the 5’ end, etc.) Therefore, by reading the gel bands
from smallest to largest, we can determine the 5’ to 3’ sequence of the original
DNA strand.

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 Now, let us understand the interpretation of the DNA sequence shown in figure 11.
Autoradiography of DNA fragments. Arrange the bands according to their size. Smallest
fragment is found at the bottom of the autoradiography and largest fragment is found at
the top. We will read the sequence from bottom to top according to their increasing
size. Shortest fragment is in the Adenine and largest fragment is in the Cytosine.
The newly synthesized strand DNA sequence read ATGCACTTGATC the direction is
5’ to 3’, which is complementary to given DNA template strand TACGTGAACTAG
the direction is 3’ to 5.’

Largest fragment TOP

Direction of
reading the
sequence

Smallest fragment BOTTOM

Figure 11. Autoradiography of DNA fragments

Outcomes of Human Genome Project

 There are approximately 22,300 protein-coding genes in human beings, the same
range as in other mammals. Mouse– 23,000 genes (approximately)
 Drosophila– 17,000 genes ( approximately), C.elegans -< 22,000 genes
 We share many homologous genes (called “orthologs”) with both these animals, by
alternative.

The public availability of a complete human genome sequence and other organisms,
represented a defining moment for both the biomedical community and for society.
The human genome database has enabled the identification of variety of genes that are
associated with disease. This has enabled more objective and accurate diagnoses.
Here are some applications of Human Genome Project in different field of sciences.

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Application of Human Genome Project in the Field of Sciences
Medicine
Improvements in diagnostic and therapeutic applications. Implementation of
preventative measures and increases in gene therapy applications.
Biotechnology
It is the production of useful protein products for use in medicine, agriculture,
bioremediation and pharmaceutical industries. Examples include antibiotics, protein
replacement (factor VII, TPA, Streptokinase, insulin, interferon). BT insecticide
toxin (from Bacillus thuringiensis– bacteria) Herbicide resistance (glyphosate
resistance). Bioengineered foods (e.g. Flavr Savr tomato, antisense - poly
galacturonate to delay rotting).
Bioinformatics
The newest, fastest growing field of concentration in the life sciences that
integrates biotechnology and computer science to determine gene function,
regulation and control, DNA sequence assembly and analysis using computer
based techniques is involved. Unknown gene sequences can be compared to
databases of known genes determination of an unidentified function.
Proteomics
Probes the patterns and levels of gene expression in diseased cells that
can be analyzed to build databases of expression profiles.
Pharmacogenomics
Investigates SNPs and DNA mutations associated with disease susceptibility
and drug sensitivities.
Developmental Biology
Regulation of embryonic development and the aging process.
Evolutionary and Comparative Biology
Comparisons of DNA between different organisms can provide evolutionary
histories, since DNA mutates at a constant rate.

What’s More

Independent Activity 1
JOURNEY BACK IN TIME
You are tasked to create a timeline that would showcase the important event that
helped shape the field of the Human Genome Project. Aside from the information given
in this module, you are strongly encouraged to do some research work on the internet or
other book references.

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 A word bank containing the list of dates, and their respective achievements will be
given to guide you on your task. Write your answers on a separate sheet of paper.

SIGNIFICANT DATES IN THE HUMAN GENOME PROJECT

1970 1985 1986 1989 1990 1993 1994 1995
1996 1997 1998 1999 2000 2001 2002 2003

MILESTONES IN HUMAN GENOME PROJECT

U.S. President Clinton and UK’s PM Working draft of human genome

Blair support free access to genome sequence was published in “The
information. Nature and Science”.
The U.S. Department of Energy Developed a technique for DNA
and the National Institute of Health sequencing, known as the Sanger’s
came forward to fund the Human method of DNA sequencing.
Genome Project.
HGP was officially launched with HGP’s Human Genetic Mapping
James Watson as its Project Director. goal was achieved.
Human Genome Project ended with First fifth (5th)year plan for HGP
all the goal achieved. was published.
Yeast genome was sequenced. Genetic privacy act was passed.
Working draft of mouse genome Sequencing of human chromosomes
sequence was completed and 22 was completed and published in
published. “The Nature”.
Japan’s Riken Genome Service was U.K.”s medical research council
established. (MRC) joined the Human Genome
Project
Proposed the idea of sequencing the NIH becomes NHGRI. Escherichia
human genome. coli genome sequenced.

Use this as a guide in answering your activity. Take note that you can be creative in
presenting your timeline.

Date MILESTONES IN HUMAN GENOME PROJECT

1970 Fredrick Sanger developed a technique for DNA sequencing,

known as the Sanger’s method of DNA sequencing.

17
Independent Assessment 1
TAXONOMY OF THE MAPPING THE GENOME

Directions: Write a word or phrase for each letter of the alphabet which is/are related to
the topic human genome, gene mapping, gene identification, and DNA
sequencing.

Letter Word/Phrase Letter Word/Phrase

A N
B O
C P
D Q
E R
F S
G T
H U
I V
J W
K X
L Y
M Z

Independent Activity 2
FACT or BLUFF
Directions: Identify whether the given statements are correct or not. Write FACT if the
statement is correct and write BLUFF if the statement is incorrect. Then
underline the word which makes the statement wrong. Write each
statement and your answer on a separate sheet of paper.
_____1. Genetic map is an illustration that lists genes and their location on
a chromosome.
_____2. Cytogenetic mapping used the information obtained by macroscopic analysis
of stained sections of the chromosome.
_____3. Gene mapping can be used in a variety of other applications, such as
using live microbes to clean up pollutants or even prevent pollution.
_____4. Physical maps present the intimate details of larger regions of
the chromosomes.
_____5. Saliva is the common sample used in personal genomic test.

18
_____6. The sub-segments of these that start from start codon (ATG) are ORFs.
_____7. Gene prediction refers to the process of identifying the regions of genomic
DNA that encode DNA.
_____8. Open Reading Frame will typically consist of at least 100 codons equivalent to
300 nucleotides.
_____9. Empirical method is searched for sequence that are similar to intrinsic
evidence in the form of known expressed sequence tags, mRNA, and protein
code products.
_____10. Ab initio method is an extrinsic method based on the gene content and signal
detection.

Independent Assessment 2
Match my Function!
Directions: Match the description in Column A to its respective term in column B. Write
the letter of the correct answer in a separate sheet of paper.

Column A Column B
_____1. Process of finding the locations of A. Ab Initio Method
genes on each chromosomes. B. Cytogenic Mapping

_____2. Study the entire genomes. C. Empirical Method

_____3. A gene sequence on chromosome that D. Gene Mapping
co-segregates with specific traits. E. Gene Identification
_____4. It overcomes the limitation of genetic F. Genetic marker
mapping and not affected by changes in G. Genomics
recombination of frequency. H. Open Reading Frames
_____5. It reflects sequence differences in DNA I. Radiation hybrid mapping
sites which cleaved by restriction enzymes. J. Restriction Fragments

_____6. Used information obtained by microscopic Length of Polymorphisms

analysis of stained sections of the chromosomes.
_____7. Process of identifying the regions of genomic
DNA that encode genes.
_____8. A part of a reading frame that has the ability to be
translated.
_____9. Intrinsic method based on gene content and
signal detection.
_____10. Extrinsic evidence in the form known expressed
of sequence tags, mRNA, and homologous sequence.

19
Independent Activity 3
SANGER SEQUENCING METHOD
Objectives:
After performing this activity, you should be able to:
1. analyze and read a gel electrophoresis sequence; and
2. perform the Sanger sequencing method through gel electrophoresis.

Materials needed:
colored pencil/crayon, bond paper, ruler

Procedures:
3’ 5’
1. Use this ACGGGACTACCA a single stranded DNA sequence from 3’ to 5’,
consisting of 12 deoxyribonucleotides.
2. Write down the primer 5’ to 3’ direction which is complementary to the given single
stranded DNA sequence.
3. Write "A" Reaction Tube (contains dideoxy adenine), "T" Reaction Tube (contains
dideoxy thymine), "C" Reaction Tube (contains dideoxy cytosine) and "G" Reaction
Tube (contains dideoxy guanine) . Write down all the possible complementary
strand lengths that terminate with the dideoxy analogue present in the reaction tube.
4. Next count the number of nucleotides in each fragment that you "synthesized" and
write it down next to the fragment. Note that all the fragment sizes are different.
5. Now list the fragment sizes in order, the numbers should be sequential from 1-12.
6. On your paper construct the pattern of gel electrophoresis as shown below. Draw the
DNA fragments according to size in the four (4) lanes, corresponding to the four
reaction tubes. Lane M stands for the marker (run to know the sizes of the fragments).
Now you will read the sequence of nucleotides from the bottom up. The sequence
that is read is the COMPLEMENT to the DNA that was sequenced. Write down the
sequence of the DNA from the gel electrophoresis.

M A C G T
12
11
10
9
8
7
6
5
4
3
2
1
Figure 12. Pattern of Gel electrophoresis

20
Guide Questions:
1. What type of DNA sequence did you use in this activity?
2. What is the newly synthesized DNA sequence that can be transcribed from the
above DNA template strand ?
3. How many DNA fragments were formed?
4. Are the sizes of fragments the same? Why does the length of fragments vary in
size?
5. What is Sanger sequencing method?

Independent Assessment 3
ORGANIZE ME!
Directions: Fill in the graphic organizer to complete the process of Sanger Sequencing
Method. Arrange the jumbled letters and choose your answer from the
box provided below. Write your answer on a separate sheet of paper.

Steps in Sanger DNA

Sequencing

C R P N A P I L A C I F I O T I M

N D A N I O C A R T E X T
1. _____________________

N O I T A C I F I T N E D I F
O E T H D E I F I L P M A
R F A G E M N T S

2. _____________________

3. _____________________

21
 What I Have Learned

Directions: Let us frame now what you have learned in this lesson as you go over the
following statements. Fill in the blanks with the best answer.
FRAMING CONCEPTS IN MAPPING THE GENOME

I have learned that the Human Genome Project is _________________________.

The HGP aimed to map all the genes in ______________, determine the sequences of
the __________________ that make up the human DNA. Also to sequence the
genomes of other organisms that are important in medical research such as ________,
and __________.
HGP is important in medicine because ______________________and in other
field of sciences such as __________,_________,_________,_________,________
and ____________.
_________ succeeded James Watson in 1993 as the overall Project head and
the director of the National Institute Health and was power until the ______________in
2003.
Gene Mapping is ___________________________________________________,
_______________ is the process of identifying the target genes while DNA sequence is
____________________________________________________________. These are
the techniques used in the Human Genome Project which ended with the achievement
of goals, hence, I learned to the appreciate its importance.

What I Can Do

TROPICANA HYBRID TEA ROSE, (Rosta tropicana): Glyceraldehyde-3-phosphate

dehydrogenase (GAPDH) GGTAACCTAAAGGGAATCCTCG.

G G T A A C C T A A A G G G A A

T C C T C G

About this gene: This sequence is part of a gene called GAPDH which is
important for metabolism as it breaks down sugar (glucose) and helps turn them into
energy.

22
 Base Pairing Rules

A Pair with T C Pair with G

DNA has four units or “bases” known as A for Adenine, Cytosine for C,
Guanine for G, and Thymine for T. Each base binds with only one partner: A with T; C
with G. Your sequence bracelet should follow the same rules; look in the circles above to
work out which colored beads you should use. Your bracelet will contain two strands of
beads that match up the same way the units (or bases) in DNA do. That means if you
know the sequence of one strand, you can work out the sequence of the other.
Materials needed:
Four colors of beads (red, green, yellow and blue) TAKE Use the cutter
Elastic string (60 cm long) or scissor with
NOTE care.
Scissors
Procedures:
1.
2. Tie a knot about 5 cm from one end of each string; then tie the two strings together at
the knots.
3. Use the gene sequence of Tropicana hybrid tea rose. Look at the first letter in your
sequence and find the right color bead to thread.
4. Thread that bead on to string 1 and thread the bead for the matching base on to string
2 (see the pairing rules sheet for guidance).
5. Keep threading beads according to your sequence until you’ve finished the sequence
on your card.
6. Knot each string after the last bead, and then tie the two new knots together.
7. Now tie the ends of your double-stranded sequence bracelet together. You’ve
finished! Congratulations! You will be graded using the rubrics below.

Rubrics for My DIY DNA Sequence Bracelet

Criteria 5 points 4 points 3 points 2 points

1. Followed directions carefully.

2. Used creativity in making DNA

sequence bracelet.
3. Displayed effort in making the
DNA sequence bracelet.

4. Be resourceful in making DNA

sequence bracelet.

Total Score:

23
 Assessment

Directions: Read each question carefully. Write the CAPITAL letter of your choice on
a separate sheet of paper.

1. Which of the following refers to the study of the entire genomes?

A. Anatomy C. Genetics
B. Cell biology D. Genomics

2. Which of the following describes the Human Genome Project?

A. An international collaborative research program whose aimed to complete mapping
and understanding of all the genes of human beings.
B. It involves sequencing the genomes of small number of individuals and then
assembling these together to get a complete sequence for each chromosome.
C. It operates from 1990 t0 2003, which provides the researchers with basic
information the sequence of the three billion chemical base pairs the make up
human genomic DNA.
D. All of the above.

3. Who proposed the idea of sequencing the human genome ?

A. Charles DeLisi C. James Watson
B. Fredrick Sanger D. Robert Sinsheimer

4. When was the version of human genome sequence completed?

A. 2000 B. 2001 C. 2002 D. 2003

5. Which of the following application of the Human Genome Project does not affect the
field of bioinformatics?
A. Investigates patterns and levels of gene expression in diseased cells that can
be analyzed to build databases of expression profiles.
B. Involved in DNA sequence assembly and analysis using computer based
techniques to determine gene function, regulation and control.
C. The newest, fastest growing specialty in the life sciences that integrates
biotechnology and computer science.
D. Unknown gene sequences can be compared to databases of known genes
determination of an un identified function.

6. Approximately how many coding - protein genes are there in human being?
A. 22,300 B. 23,000 C. 23,300 D. 24,000

7. Which of the following refers to the process of finding the location of a particular gene
on a chromosome?
A. DNA Sequencing C. Gene Identification
B. DNA Fingerprinting D. Gene Mapping
24
8. Which of the following genetic marker is NOT used in generating genetic map?
A. Microsatellite Polymorphisms C.RFLPs
B. Physical Maps D. VNTRs

9. How do genetic map and physical map are related with each other?
A. They provide the outline and physical details of chromosome.
B. They are necessary tool in mapping the disease genes.
C. They are collection of genetic markers and gene loci, and required to build
complete picture of genome.
D. They develop the genetic markers and a mapping population.

10. Which of the following refers to the process of identifying the regions of genomic
DNA that encode genes?
A. DNA Sequencing C. Gene Mapping
B. Gene Identification D. Open Reading Frame

11. Which of the following is NOT a way to identify the Open Reading Frames?
A. Gene sequence are largely conserved - so if ORF sequence is present in multiple
genomes, it likely represents a gene.
B. Locate a sequence corresponding to a start codon (ATG) in order to determine the
reading frame.
C. Read this sequence in base triplets until a stop codon is reached. (TAG,TGA or
TAA)
D. The longer the sequence, the more significant the likelihood that the sequence
corresponds to an open reading frame.

12. What is the role of bioinformatics in identifying target genes?

A. It can automatically identify the potential start and stop codons.
B. It can conserve gene sequence if ORF sequence is present in multiple genomes.
C. Locate a sequence corresponding to a start codon (ATG) in order to determine the
reading frame.
D. Target genes can be identified by searching online databases for long stretches of
DNA that could potentially code to protein.

13. Which of the following processes does not belong to the steps of Sanger DNA
Sequencing?
A. DNA extraction
B. Identification of the amplified fragments
C. PCR amplification
D. Pyrosequencing

14. What are the basic requirements for in vitro DNA synthesis?
A. DNA template strand, primer, deoxynucleotides and DNA polymerase.
B. DNA template strand, primer, dideoxynucleotides and DNA polymerase.
C. DNA template strand, primer, deoxynucleotides and DNA extraction.
D. DNA template strand, primer, deoxynucleotides and PCR reagents.

25
15. Which of the following is also called High-Throughput Sequencing?
A. Automated DNA Sequencing
B. Maxam-Gilbert Method
C. Next-Generation Sequencing
D. Sanger Sequencing Method

Additional Activities

Directions: Coronavirus disease or Covid-19 is a new public health crisis facing the
world today and threatening the human lives. In a separate sheet of paper,
explain the importance of the Human Genome Project to make a vaccine
for anti- Coronavirus disease. You will be graded using the rubrics below.

RUBRICS FOR ESSAY

Scale Level of Mastery Description

Able to write 250 words or more and shows deep

10 High Mastery
understanding through cohesive ideas.
Able to write 200 words and shows understanding through
8 Mastery
mostly cohesive ideas.
Approaching Able to write 150 words and shows understanding through
6
Mastery some cohesive ideas.
Able to write 100 words and shows understanding through
5 Low Mastery
a few cohesive ideas.

Able to write 50 words and shows a little understanding

3 No Mastery
through a few ideas.

26
 27
7. BLUFF Genes not DNA 3. 5’ TGCCCTGATG 3’ in which target DNA tem-
plate strand is denatured
8. FACT 4. 5’ TGCCCTGATGG 3’ and annealed to anoligonu-
9. BLUFF Extrinsic not intrinsic List of fragments from smallest cleotide primer, which is
to longest sequence then extended by DNA pol-
10. BLUFF Intrinsic not extrin- ymerase using a mixture of
sic 1. 5’ T 3’ deoxynucleotides triphos-
phates (normal dNTPs) and
Independent Assessment 2 2. 5’ TG 3’ chain-terminating dideox-
1. D 3. 5’ TGC 3’ ynucleotides triphosphates
(ddNTPs).
2. G 4. 5’ TGCC 3’
Independent Assessment 3
3. F 5. 5’ TGCCC 3’
1. DNA extraction
4. I 6. 5’ TGCCCT 3’
2. PCR amplification
5. J 7. 5’ TGCCCTG 3’
3. Identification of the ampli-
6. B 8. 5’ TGCCCTGA 3’ fied fragments
7. E 9. 5’ TGCCCTGAT 3’ What I Have Learned
8. H 10. 5’ TGCCCTGATG 3’ Answer may vary
9. A 11. 5’ TGCCCTGATGG 3’ Assessment
10. C 12. 5’ TGCCCTGATGGT 3’ 1. D
Independent Activity 3 M A C G T 2. D
12 ----- 3. D
“ A” REACTION TUBE
11 -----
(Contains dideoxy Adenine) 10 ----- 4. D
1. 5’ TGCCCTGA 3’ 9 -----
5. A
8 -----
“ T” REACTION TUBE 7 ----- 6. A
(Contains dideoxy Thymine) 6 -----
5 ----- 7. D
1. 5’ T 3’
4 ----- 8. B
2. 5’ TGCCCT 3’ 3 -----
2 ----- 9. C
3. 5’ TGCCCTGAT 3’ 1 ----- 10. B
4. 5’ TGCCCTGATGGT 3’
Guide Questions: 11. A
“ C” REACTION TUBE
(Contains dideoxy Cytosine) 1. 3’ ACGGGACTACCA 5’ 12. D
1. 5’ TGC 3’ 2. 5’ TGCCCTGATGGT 3’ 13. D
2. 5’ TGCC 3’ 3. Twelve (12) fragments were 14. A
formed. 15. C
3. 5’ TGCCC 3’
4. No. The fragment sizes are
“ G” REACTION TUBE
different because each one cor-
(Contains dideoxy Guanine) responds to a different nucleo-
1. 5’ TG 3’ tide location on the DNA to be
sequenced.
2. 5’ TGCCCTG 3’
5. Sanger sequencing method
Answer Key
 28
What I know What’s more
Part A Independent Activity 1
1. D JOURNEY BACK IN TIME
2. B Date Events
3. B 1970 Fredrick Sanger developed a technique for DNA se-
quencing, known as the Sanger’s method of DNA
4. B sequencing.
5. A 1985 Proposed the idea of sequencing the human genome.
Part B 1986 The U.S. Department of Energy and the National
Institute of Health came forward to fund the Human
1. True Genome Project.
1989 U.K.’s medical research council (MRC) joined the Hu-
2. True man Genome Project.
3. False 1990 HGP was officially launched with James Watson as its
Project Director.
4. False 1993 First fifth (5th)year plan for HGP was published.
5. True 1994 HGP’s Human Genetic Mapping goal was achieved.
6. True 1995 Genetic privacy act was passed.
7. False 1996 Yeast genome was sequenced.
8. False 1997 NIH becomes NHGRI. Escherichia coli genome se-
quenced.
9, True 1998 Japan’s Riken Genome Services was established
10. True 1999 Sequencing of human chromosomes 22 was complet-
ed and published in “The Nature”.
2000 U.S. President Clinton and UK’s PM Blair support
free access to genome information.
What’s In
2001 Working draft of human genome sequence was pub-
1. Paternity and Maternity lished in “ the Nature and Science”.
Test 2002 Working draft of mouse genome sequence was com-
pleted and published
2. Diagnosis of Inherited 2003 Human Genome Project ended with all the goal
Disorders achieved.
3. Breeding Program
Independent Assessment 1
4. Personal Identification
TAXONOMY OF THE MAPPING THE
5. Development of Cures for Inherited disorders
GENOME
6. Forensic Science
Answers may vary
Independent Activity 2
What’s New FACT OR BLUFF
1. Genome 1. FACT
2. Mapping 2. BLUFF Microscopic not macroscopic.
3. Nucleotides 3. FACT
4. Sequencing 4. BLUFF Smaller not larger
5. Termination 5. FACT
Hidden word : The Human Genome Project 6. FACT
 References

Cornell, B. “Gene Identification” 2016. Accessed January 08, 2021 https://ib.bioninja.com.au/

options/untitled/b2-biotechnology-in-agricul/gene-identification.html?
fbclid=IwAR3vgJgWaCKdScm4HrI-BFSfLMo3JK3D_3GTJUPwhbUCkpPOAncK31dSbW4

Kelsey Wood. “How to make a DNA Bracelet” April 26, 2017. Accessed January 08, 2021 https://
blog.aspb.org/how-to-make-a-dna-bracelet/?
fbclid=IwAR0Lyly6CMT8I2G5BeXr9Gk2HqeBv7XtIV6ixwao-Eru6RjtzMXuEGfR_6Q
Harsha, Joseph. “DNA Sequencing- Sanger's Method” Feb 3, 2018. Accessed January 08, 2021
https://www.slideshare.net/HarshaJoseph2/dna-sequencing-sangers-method?
fbclid=IwAR32s14jc0KPPQuOxWbVzLRYW5QKUTmZXcm9QoEtb2d4Lo_a2oao3dCKQn0
Judith L. Fridovich-Keil. “Human Genome Project” 1990-2003. Accessed January 09, 2021 https://
www.britannica.com/event/Human-Genome-Project
Wikipedia, the free encyclopedia. “Gene Prediction” February 2021. Accessed February
10, 2021 https://en.wikipedia.org/wiki/Gene_prediction?
fbclid=IwAR1eP6UgrkiAcGmE3hwGirdTIuTyFR5ZgfFQhMS1ixm55GQubU7Q0phv_m8
Lumen Learning. “Mapping Genomes” No Date Available. Accessed February 4, 2021 https://
courses.lumenlearning.com/sanjacinto-biology1/chapter/mapping-genomes/?
fbclid=IwAR32s14jc0KPPQuOxWbVzLRYW5QKUTmZXcm9QoEtb2d4Lo_a2oao3dCKQn0
Frank Lectures. “How Sanger Works – Classic Sanger Method” May 25, 2019. Ac-
cessed February 5, 2021 https://www.youtube.com/watch
app=desktop&v=QIMkQ4E_wE&fbclid=IwAR03r1Z9rB3K6G7WtUrX1e0RzUeBlI4uZrZTZ9
EgWm4r8Gd2Rk4dqBpHOm0+

Sagar Aryal. “DNA Fingerprinting- Principle, Methods, Applications” September 4, 2018. Accessed
February 4, 2021 https://DNA Fingerprinting- Principle, Methods, Applications | Molecular
Biology | Microbe Notes

29
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Curriculum Implementation Division
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