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 ABOUT THE MODULE
This module contains four (4) chapters. Each chapter corresponds to a grading quarter. Chapters contain
lessons which are specifically designed and reformatted to coincide with the new normal in learning (i.e.
blended learning, modular approach). Parts of the lesson consist of the following:
At the beginning of every lesson in this module, you will be
provided with warm-up activities to get you started. This provides
overview of the lesson some in situational formats as closest as it
Start-up
gets to the students’ experiences. These are thought-provoking and
Activity
engaging activities that serve as motivation and prelude to the
lesson.

This section introduces the new lesson, topic, or content you need
to learn. This provides you in-depth discussion, readings,
Topic exposition of the content. This also provides the materials for
Content reading. As you learn and explore the material, you are
encouraged to elicit or perform quick exercises.

This part includes recall of concepts and shows interconnectedness

of ideas. This part may serve as the starting point of student-
Go! teacher discussion online as this checks comprehension of the
content.

This contains additional tasks and may include post tests and lesson
quiz for higher learning retention. This serves as “boosters” of the
Activity
learned skills or content through adequate and appropriate practice
Exercises
exercises and activities.

This provides more activities for reinforcement and engagement

Almost
with the topic at hand.
there!
At this point, the students finish the required tasks and lesson. This
section may provide lesson summary, precise or points to ponder.
You are a
The students are also encouraged to engage in reflective exercises
Finisher!
such as jotting their learnings through mind maps.

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GRADE 12 – SHS GENERAL BIOLOGY 2 - MOST ESSENTIAL LEARNING COMPETENCES (MELC) AS TO
DEPED GUIDE FOR COVID 19 REPONSE

Week of
the
CONTENT Quarter / MOST ESSENTIAL LEARNING COMPETENCES
Grading
Period
Q3/ W1 Outline the processes involved in genetic engineering
Recombinant DNA
Q3/ W1 Discuss the applications of recombinant DNA
Describe general features of the history of life on Earth, including
generally accepted dates and sequence of the geologic time scale and
Q3/ W2
characteristics of major groups of organisms present during these time
periods
Explain the mechanisms that produce change in populations from
Relevance, Q3/ W2 generation to generation (e.g., artificial selection, natural selection,
Mechanisms, genetic drift, mutation, recombination)
Evidence/Bases, Show patterns of descent with modification from common ancestors to
Q3/ W3
and Theories of produce the organismal diversity observed today
Evolution
Q3/ W3 Trace the development of evolutionary thought
Explain evidences of evolution (e.g., biogeography, fossil record,
Q3/ W4
DNA/protein sequences, homology, and embryology)
Infer evolutionary relationships among organisms using the evidence of
Q3/ W4
evolution
Basic Taxonomic Explain how the structural and developmental characteristics and
Q3/ W5
Concepts and relatedness of DNA sequences are used in classifying living things
Principles, Identify the unique/distinctive characteristics of a specific taxon relative
Description, Q3/ W5-6
to other taxa
Nomenclature,
Identification, and Describe species diversity and cladistics, including the types of evidence
Q3/ W6
Classification and procedures that can be used to establish evolutionary relationships
Compare and contrast the following processes in plants and animals:
Plant and Animal reproduction, development, nutrition, gas exchange, transport/circulation,
Organ Systems and Q4/ W1-4 regulation of body fluids, chemical and nervous control, immune systems,
their Functions and sensory and motor mechanisms

Explain how some organisms maintain steady internal conditions (e.g.,

Feedback temperature regulation, osmotic balance and glucose levels) that possess
Q4/ W5-6
Mechanisms various structures and processes

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 QUARTER 1 - GENETICS
LESSON 1
GENETIC ENGINEERING
I. INTRODUCTION

In order to survive, man has successfully

domesticated selected plants and animals. He has
taken an active part in choosing desired traits of
plants and animals. Traits that were considered
valuable (i.e. high fruit yield; high milk production,
etc.) were sought out and propagated. The processes
involved may include classical breeding practices
such as controlled pollination of plants, and the
mating of animals with desired traits. In today’s
modern science, molecular biology techniques are
being employed in the insertion and expression of
proteins in different organisms for various purposes.

II. START-UP ACTIVITY

Traits that I admire

Place the specific traits that you like in Plants and Animals in the table below.
Plants Desirable Traits Animals Desirable Traits
1. Root systems are well formed 1. Adaptability
2. Firm leaves 2. Robustness
3. No sign of pest and diseases 3. Disease resistance
4. Foliage growth 4. Domesticated
5. Well-formed flowers and fruit 5. Vitality

Study the table below, how do you think each of the traits was introduced or developed (i.e., classical breeding or
recombinant DNA technology).
ENHANCED TRAIT MODIFYING TECHNIQUE
Kobe / Wagyu Beef (Beef with good fat distribution) Classical breeding
Guapple (Large sized guava) Classical breeding
Human Insulin-producing bacteria Recombinant DNA Technology
Flavr-Savr (Delayed-ripening tomatoes) Recombinant DNA Technology
Macapuno trait in coconuts Classical breeding

What comes in to your mind when you heard the word classical breeding? Kindly site some examples.
It involves the intentional interbreeding (crossing) of closely or distantly related individuals in
order to create new crop varieties or lines with desirable traits.

Example: The purpose of crossing a mildew resistant pea with a high-yielding but sensitive pea is to
provide mildew resistance without compromising the high-yield features.

What comes in to your mind when you heard the word Recombinant DNA Technology? Kindly site some
examples.
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 It includes modifying genetic material outside of an organism in order to get enhanced and
desired qualities in living creatures or their products.

Example: Antibiotics and other biological agents such as insulin, Hepatitis B vaccination, human
growth hormone, and erythropoietin are manufactured in the pharmaceutical industry.

How do you think they differ from each other?

Classic breeding involves the intentional interbreeding (crossing) of closely or distantly related
individuals in order to create new crop varieties or lines with desirable traits while Recombinant DNA
Technology involves the insertion of DNA fragments from a number of sources into a vector with a
desired gene sequence.

III. TOPIC CONTENT

What is GENETIC ENGINEERING?

Genetic engineering is the artificial manipulation,

modification, and recombination of DNA or other nucleic acid
molecules in order to modify an organism or population of
organisms. It is the process of using recombinant DNA (rDNA)
technology to alter the genetic makeup of an organism. The term
genetic engineering initially referred to various techniques used for
the modification or manipulation of organisms through the
processes of heredity and reproduction. As such, the term
embraced both artificial selection and all the interventions of
biomedical techniques, among them artificial insemination, in vitro
fertilization (e.g., “test-tube” babies), cloning, and gene
manipulation.
Traditionally, humans have manipulated genomes indirectly by controlling breeding and selecting offspring with
desired traits. Genetic engineering involves the direct manipulation of one or more genes. Most often, a gene from
another species is added to an organism's genome to give it a desired phenotype. Same is true with classical plant
breeding that uses deliberate interbreeding (crossing) of closely or distantly related individuals to produce new crop
varieties or lines with desirable properties.

Classical breeding practices focus on the mating of organisms with desirable qualities.
Genetic engineering involves the use of molecular techniques to modify the traits of a target organism. The
modification of traits may involve:
A. introduction of new traits into an organism
B. enhancement of a present trait by increasing the expression of the desired gene
C. enhancement of a present trait by disrupting the inhibition of the desired genes’ expression.

A general outline of recombinant DNA may be given as follows:

A. cutting or cleavage of DNA by restriction enzymes (REs)
B. selection of an appropriate vector or vehicle which would propagate the recombinant DNA ( eg. circular
plasmid in bacteria with a foreign gene of interest)
C. ligation (join together) of the gene of interest (eg. from animal) with the vector (cut bacterial plasmid)
D. transfer of the recombinant plasmid into a host cell (that would carry out replication to make huge copies
of the recombined plasmid)
E. selection process to screen which cells actually contain the gene of interest
F. sequencing of the gene to find out the primary structure of the protein

Ways in which these plasmids may be introduced into host organisms:

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 BIOLISTICS. In this technique, a “gene gun” is used to fire DNA-coated pellets on plant tissues. Cells that
survive the bombardment, and are able to take up the expression plasmid coated pellets and acquire the ability to
express the designed protein.

PLASMID INSERTION by Heat Shock Treatment. Heat Shock Treatment is a process used to transfer
plasmid DNA into bacteria. The target cells are pre-treated before the procedure to increase the pore sizes of their
plasma membranes. This pretreatment (usually with CaCl2) is said to make the cells “competent” for accepting the
plasmid DNA. After the cells are made competent, they are incubated with the desired plasmid at about 4°C for about
30min. The plasmids concentrate near the cells during this time. Afterwards, a “Heat Shock” is done on the plasmid-
cell solution by incubating it at 42°C for 1 minute then back to 4°C for 2 minutes. The rapid rise and drop of
temperature is believed to increase and decrease the pore sizes in the membrane. The plasmid DNA near the
membrane surface are taken into the cells by this process. The cells that took up the plasmids acquire new traits and
are said to be “transformed”.

ELECTROPORATION. This technique follows a similar methodology as Heat Shock Treatment, but, the
expansion of the membrane pores is done through an electric “shock”. This method is commonly used for insertion of
genes into mammalian cells.

Some methods to screen recombinant cells are as follows:

 Selection of plasmid DNA containing cells
A selection marker within the inserted plasmid DNA sequence allows the selection of “transformants”.
Usually, an antibiotic resistance gene (e.g. AMP ampicillin resistance gene) is included in the plasmid DNA. This
allows only “transformed” cells to survive in the presence of the antibiotic (e.g. ampicillin). Plating the plasmid-cell
solution on antibiotic-containing media will select for these “transformants” and only allow plasmid-containing cells
to grow and propagate into colonies.

 Selection of transformed cells with the desired gene

Certain inserted genes within the plasmids provide visible proof of their presence. These include the antibiotic
resistance genes that allow for the selection of the transformed cells within the solution. Some inserted genes also
produce colored (e.g. chromogenic proteins) or fluorescent products (e.g. GFP) that label the colonies/cells with the
inserted gene.
In some cases, the location of the cloning site within the plasmid is in the middle of a gene (i.e. β-
galactosidase, lacZ) that generates a (blue) colored product in the presence of a substrate (i.e. isopropyl β-D-1
thiogalactopyranoside, or IPTG). Cells transformed with these “empty” plasmids will turn blue in the presence of
IPTG. Insertion of a gene in the cloning site disrupts the sequence of the β-galactosidase gene and prevents the
generation of the colored product in the presence of the substrate. Cells transformed with the disrupted β-galactosidase
gene will remain “white” in the presence of IPTG. This “blue-white screening” protocol is thus able to screen for cells
that were transformed with the desired gene in the cloning site.

 PCR detection of plasmid DNA

Alternatively, the presence of the desired gene in the inserted plasmids may be confirmed using PCR
amplification. PCR reactions specific for the desired gene may be done using DNA from cells. Amplification of the
expected product would confirm the presence of the gene within the samples. PCR reactions specific for plasmid
sequences will also confirm/identify the type of plasmid used for the transformation.

 Genetically Modified Organisms (GMOs)

With the ability to insert gene sequences, comes the possibility of providing new traits for these target organisms.
This has allowed the development of GMOs. Some of these genetic modifications promise higher product yield for
their targets. These include the Flavr-Savr Tomato and Bt-Corn.

IV. ACTIVITY EXCERCISE

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PERFORMANCE TASK: 1.
Instruction: Research on the pros and cons of genetic engineering.

PROS CONS
1. Getting Rid of All Illnesses in Young and Unborn 1. It can create less nutritional value in some foods
Children
2. Tackling and Defeating Diseases 2. It could create unpredictable outcomes
3. Potential to Live Longer 3. It could be used for abusive purposes
4. Produce New Foods 4. Limits Genetic Diversity
5. Organisms Can be ‘Tailor-Made’ 5. Reduced Nutritional Value
6. Faster Growth in Animals and Plants 6. Risky Pathogens
7. Pest and Disease Resistance 7. Negative Side Effects
8. It is a process that could improve human health at 8. It can put agricultural workers at risk for financial
the cellular level harm
9.  It can boost the positive traits in every life form 9. It could interact negatively with other species
10. It can be used to help current food resources to 10. It could create new diseases
begin producing more of them

2. What is your opinion on Genetic Engineering? Note: Support your opinion with facts and include the issue of
biosafety.

Genetic Engineering is a technology that uses molecular cloning and

transformation to change the structure and nature of genes in humans, animals,
and foods. To put it another way, it is the process of adding or changing DNA in
an organism to cause significant changes. Taking parts of DNA and mixing them
with other pieces of DNA is what genetic engineering, broadly defined, entails.
[This] is something you manufacture in your own laboratory using test tubes,
rather than something that occurs naturally. Then taking what you've created
and propagating it in a variety of creatures ranging from bacteria to yeast cells
to plants and animals

3. Determine which technologies are most appropriate for which cell types.

TECHNOLOGY CELL TYPE

1.Biolistic Plants cells
2. Electroporation Mammalian cells
3. Biolistic Mammalian cells
4. Heat Shock Treatment Bacterial cells
5. Heat Shock Treatment Mammalian cells

RECOMMENDED READINGS:
1. https://www.ck12.org/book/human-biology-genetics/section/10.1/
2.https://www.ck12.org/c/biology/biotechnology/lesson/BiotechnologyBIO/?referrer=concept_details
3.https://www.khanacademy.org/science/biology/biotech-dna-technology/intro-to-biotechtutorial/a/intro-to-biotechnology

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 LESSON 2
APPLICATIONS OF RECOMBINANT DNA

I. INTRODUCTION

Different organisms have different traits based on their genes (DNA sequences). For example, frogs have
antimicrobial peptides on their skin. Some jellyfish have proteins that allow them to glow in the dark. Mutations in
hemoglobin genes lead to anemia.

Based on the central dogma, if transcription and translation of genes lead to some traits, then the insertion of
certain genes in a given organism may provide it with new traits. This is the basis for the development of genetically
modified organisms (GMOs)

II. START-UP ACTIVITY

Know them first:
Before we start lest have a quick prior knowledge on the terms that we will encounter in this topic.
Look/search and read for the definition of the following terms below:
1. Clone - an individual grown from a single somatic cell or cell nucleus and genetically identical to it.
2. Modified Trait - is a laboratory-modified organism whose DNA has been altered to promote the
expression of desirable physiological features or the synthesis of desired biological products.
3. Plasmids - a genetic structure in a cell that may replicate independently of the chromosomes, usually
a tiny circular DNA strand in a bacterium's or protozoan's cytoplasm.
4. Human Genome - is the Homo sapiens genome, which is the DNA sequence contained in 23 pairs of
chromosomes in the nucleus of every diploid human cell.
5. Biotechnology - is a vast field of biology that involves the development or manufacture of things using
live systems and creatures.
6. Genetic Modified Organism - any organism whose genetic material has been altered through genetic
engineering techniques is referred to as a genetically modified organism.
7. PCR Amplification – it is a method for making millions to billions of copies of a specific DNA sample
quickly, allowing scientists to take a small sample of DNA and amplify it to a large enough amount to
investigate in detail.

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 8. Detection - it is a process of detecting, discovering, and exposing what has been concealed or hidden
or seeks to avoid notice.

PRE-ACTIVITY: Designer Genes Work

1. How does DNA Replicate?
The parental DNA is kept together during conservative replication, while the newly generated daughter
strands are kept together. Each of the two parental DNA strands acts as a template for new DNA to be
produced, according to the semi-conservative technique; following replication, each double-stranded
DNA has one parental or "old" strand and one "new" strand.
2. What is Genetically Modified Organism (GMO)?
Is any organism whose genetic material has been altered through genetic engineering techniques is
referred to as a genetically modified organism.
3. Illustrate your own Designer genes based on the following:

4. Identify the modified/ added trait.

Example: Hot Tomato > Chili > Tomato > Spicy Tomato

Tomatoes
It was reported this week that Brazilian scientists are hoping to create spicy tomatoes using Crispr gene-editing
techniques. Although tomatoes contain the genes for capsaicinoids (the chemicals that give chillies their heat)
they are dormant – Crispr could be used to make them active. This is desirable because, compared to tomatoes,
chillies are difficult to farm – and capsaicinoids have other useful applications besides their flavour – in pepper
spray for example.

https://www.theguardian.com/science/2019/jan/13/the-five-genetically-modified-fruit-edited-bananas-tomatoes

III. TOPIC CONTENT

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PRESENTATION OF RECOMBINANT DNA There are many different traits that can be introduced to organisms to
change their properties. The following table shows examples of modified traits using cloned genes and their
applications:

MODIFIED TRAIT GENE RECIPIENT APPLICATION (FIELD)

MODIFICATION ORGANISM

Insulin Production Insertion of Human Bacteria (Medicine) Production of Human Insulin in Bacteria
Insulin Gene
Pest Resistance Insertion of Bt-toxin Corn / Maize (Agriculture) Production of corn plants with increased
gene resistance to corn boxer

Delayed Ripening Disruption of a gene for e (e.g. Agriculture) Production of plants with fruits that have
a ripening enzyme (e.g. polygalacturonase) delayed ripening fruits. These fruits will survive
polygalacturonase) Tomato plant longer transport time, allowing their delivery to
further locations (i.e. export deliveries)

Chymosin Production Insertion of a gene for Bacteria (Industry) Enhance large scale production of
chymosin chymosin. This enzyme serves as a substitute for
rennet in the coagulation of milk. Rennet has to be
harvested from calves. The large scale production of
this enzyme in bacteria provides an abundant supply
of this important component for the cheese
production industry.

PCR Amplification Once a desired trait is chosen, information must be acquired for either its detection or
expression in a given organism.

1. DETECTION
Some researchers may be interested in determining if a given gene/trait is available in a particular organism. If
no previous research provides this information, researchers may test the DNA of different organisms for the presence
of these specific genes. A technique that allows the detection of specific genes in target organisms is called PCR.
PCR amplification is an in-vitro method that simulates DNA replication in vivo. It utilizes a thermostable
(heat-resistant) DNA polymerase that builds single stranded DNA strands unto unwound DNA templates.
PCR uses repeated cycles of incubation at different temperatures to promote the unwinding of the DNA
template (~95°C); the annealing of a primer (a ~20bp oligonucleotide sequence (recall RNA primers in DNA
replication) onto the ssDNA template strand (~54 - 60°C); and the extension of the generated ssDNA strand through
the binding of complementary bases to the template strand (~72° C). The thermostability of the polymerase allows it
to survive the repeated cycles of denaturation, annealing and extension with little loss of enzyme function. Each cycle
of PCR doubles the amount of the target sequence. A typical PCR experiment uses about 35 cycles of amplification.
This increases the original amount of the target sequence by 235 (i.e. ~34 billion) times.
Gene detection by PCR involves the design of primers that would only bind to sequences that are specific to a
target. For example, researchers would want to find out if gene X (e.g. the gene for insulin) is available in a target
organism (e.g. a mouse, Mus musculus). Primers may be designed by looking at the available sequences for gene X in
the databases (e.g. all the genes for insulin in different organisms; humans, pigs, cows, etc.). The different gene X
sequences must be aligned/ compared to match areas of sequence similarity (conserved sequences) and areas of
sequence dissimilarity (non-conserved sequences). Primers designed to have the same sequence as the conserved areas
will be specific for binding gene X sequences in all the target organisms. Primers designed to have the same sequence
as the non-conserved areas will only be specific for the organisms which match its sequence.

STEPS IN PCR AMPLIFICATION

Step 0: Undenatured Template ; Temp ~ 54 °"C; Template: double stranded (ds) DNA strand. Complementary
sequences are held together by H-bonds 5’ A T GCGATGAGGATATGACCCGATAGATAGAGGTATCTAGAGAT
3’ (Coding strand) 3’ T A CGCTACTCCTATACTGGGCTATCTATCTCCATAGATCTCTA 5’ (Non-coding strand)

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 Step 1: Template denaturation ; Temp ~ 95 °"C; Template: single stranded (ss) DNA strands; DNA strands are
separated; H-bonds between complementary sequences are broken 5’ A T
GCGATGAGGATATGACCCGATAGATAGAGGTATCTAGAGAT 3’ (Coding strand) 3’ T A
CGCTACTCCTATACTGGGCTATCTATCTCCATAGATCTCTA 5’ (Non-coding strand)’

Step 2: Primer Annealing ; Temp ~ 54 °"C (dependent on primer melting temperature); Template: ssDNA
strands. H-bonds are formed between complementary sequences on the primers and the target sequences. 5’ A T
GCGATGAGGATATGACCCGATAGATAGAGGTATCTAGAGAT 3’ (Coding strand) Direction of elongation 
CCATAGATC (Reverse Primer)
5’ GCGATGAGG 3’ → Direction of elongation (Forward Primer)
3’ T A CGCTACTCCTATACTGGGCTATCTATCTCCATAGATCTCTA 5’ (Non-coding strand)
Step 3: New DNA strand elongation ; Temp ~ 72 °"C; The two new dsDNA strands are formed by the
elongation of the generated ssDNA and the H-bonds between the complementary sequences on these new strands and
their templates. Each of the new dsDNA strands is made up of one old strand from the original template, and one new
strand that was generated as a reverse complement of the template. This is called semiconservative replication of the
sequence.

New Strand 1: 5’ A T GCGATGAGGATATGACCCGATAGATAGAGGTATCTAGAGAT 3’ (Coding

strand) (old) 3’ CGCTACTCCTATACTGGGCTATCTATCTCCATAGATC-5’ (Reverse Primer) (new)

New Strand 2: 5’ GCGATGAGGATATGACCCGATAGATAGAGGTATCTAG-3’ (Forward Primer) (new)

3’ T A CGCTACTCCTATACTGGGCTATCTATCTCCATAGATCTCTA 5’ (Non-coding strand) (old)

Step 4: Repeat step 1 to 3 for N number of cycles (N is usually 35)

PCR Results The expected product of PCR amplification will depend on the sequences / position at which the primer
sequences bind. If the forward primer starts binding at nucleotide 3 (coming from the 5’ end) of a 43bp long gene, and
the reverse primer binds at a position complementary to nucleotide 39 of the coding strand, then a 37bp product is
expected per cycle of PCR.

PCR APPLICATIONS
PCR may be used to detect the presence of a desired gene in an organism. Depending on the primer design,
the expected product may represent only a specific region of the gene or the entire gene itself. The first case is useful
for detection of the gene, or the detection of organisms with that specific gene within a sample. The second case is
useful for the amplification of the entire gene for eventual expression in other organisms. The direct
amplification/copying of a full gene is part of the process for “cloning” that gene.

2. CLONING AND EXPRESSION

Some genes provide economically, and industrially important products (e.g. insulin-coding genes; genes for
collagen degradation). In some cases, scientists would want to put these genes into organisms for the expression of
their products. One example would be the insertion of an insulin- coding gene from the human genome into bacteria.
This allows the “transformed” bacteria to now produce human insulin as a product.
Certain types of bacteria are capable of this process since they are able to take genes within their cell
membranes for eventual expression. The genes are normally in the form of small, circular DNA structures called
plasmids.

The genes found in the inserted plasmid DNA sequence will be expressed as proteins that provide specific
traits to the transformed bacteria. The basic components of an expression plasmid are listed in the following table. The
purpose of each of these is also provided.

COMPONENT PURPOSE
Promoter Allows the controlled expression of the desired gene in the presence of an inducing
agent (e.g. beta- galactosidase; heat treatment (~65°"C)

Multiple Cloning Site DNA sequence or portion for the insertion of the desired gene. This section may

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 contain sequences that will be cut by specific restriction endonucleases ( cuts within
the molecule) If both the amplified gene and the plasmid are cut with the same
restriction enzyme, then complementary sequences will be generated for each, allowing
them to bind together or anneal. The desired gene is inserted into the multiple cloning
site through this process.

Restriction enzymes cut at specific sequences.

EcoR1 Target Sequence:

5’ GAATTC 3’
3’ CTTAAG 5’

Digestion Reaction
Undigested: Digested dsDNA:

5’ GAATTC 3’ 5’ G AATTC3’
3’ CTTAAG 5’ 3’ CTTAA G5’

If the desired cut sites are not found in the gene that needs to be inserted; the sequences
can be added by including the target sequences in the primers used for PCR
amplification.

Multiple Cloning Site PCR Primers:

5’ GCGATGAGG 3’ (Forward Primer)
3’ CCATAGATC 5’ (Reverse Primer)

Forward Primer + EcoRI target sequence:

5’ GAATTCGCGATGAGG 3’
Reverse Primer + EcoRI target sequence:
3’ CCATAGATCCTTAAG 5’
Inserted Gene Successful insertion of a gene allows the expression of its protein product. This usually
Sequence provides a specific trait to the “transformed” bacteria. For example, if the gene for
Green Fluorescent Protein is placed within the expression plasmid, bacteria
transformed with this plasmid will produce protein (GFP) that will allow the bacterial
cells / colonies to glow green in the dark.

Antibiotic Resistance Provides a way to screen a population of bacteria for those that took up the plasmid.
Gene For example, if an ampicillin resistance gene is encoded in the plasmid, then only
bacteria which took up the plasmid will be able to grow on media with ampicillin.
However, if the ampicillin resistance gene is cut and the gene is inserted here for
cloning, then the cell will no longer be resistant to ampicillin. This is a way to select
which among the colony of cells actually contain the inserted gene sequence. Bacterial
cells whose ampicillin resistance gene have been cut will die in the presence (agar
plate) of ampicillin.

IV. ACTIVITY EXERCISE

ACTIVITY: 1. Illustrate the steps in restriction digestion and PCR.

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EVALUATION:

1. Discuss how PCR may be used for the detection of disease-causing pathogens in a population during the
COVID Pandemic. For example: it may be used to check if a patient has a COVID virus infection.
- The PCR test, which uses samples from blood and urine, can detect the virus early in the
disease's progression, allowing for early identification and isolation of infected people to prevent
transmission.

2. Discuss how the cloning and expression of certain genes allows for massive production of the desired
product. For Example: the cloning and expression of insulin in bacteria allows for the mass production of this
necessary protein for use by diabetic patients. Prior to insulin production in bacteria, insulin was harvested from
other animals such as pigs.
- Multiple copies of genes can be made, genes can be expressed, and individual genes can be
studied via molecular cloning. Plasmids have been extensively designed as vectors for molecular cloning
and large-scale manufacture of essential compounds like insulin.

RECOMMENDED READINGS:
1.https://flexbooks.ck12.org/cbook/ck-12-middle-school-life-science2.0/section/3.18/primary/lesson/recombinant-dna-ms-ls

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 2. https://www.ck12.org/book/cbse_biology_book_class_xii/section/14.1/
3. https://www.ck12.org/section/dna-technology

LESSON 3
HISTORY OF LIFE ON EARTH

I. INTRODUCTION

The evolutionary history of life on Earth traces the processes by which living and fossil organisms evolved, from

the earliest emergence of life to the present. Earth formed about 4.5 billion years ago (abbreviated as Ga (for gigaannum))
and evidence suggests life emerged prior to 3.7 Ga. Ago

Have you seen the movies Ice Age and The Land Before Time? How was the Earth presented in movies such as these?
Based from the movie, they described the Earth millions of years ago with:
a. covered with thick blanket of ice,
b. lots of volcanoes and high mountains,
c. large organisms roamed the land,
d. the atmosphere did not have high oxygen content,
e. asteroids/ meteors frequently hit the surface,
f. the lands moved a lot or the continents were a little closer to each other,
g. volcanic eruptions,
h. a little bit warmer,
i. plants were bigger,
j. humans were not yet around.
When did man first appear on Earth?
Well Man could have first appeared about 100 – 150 thousand years ago as shown by artefactual evidences in various
sites. The human timeline is rather flexible and debatableevery time we know a specific date, a new discovery is
announced and everything gets redated to fit the best estimates.)

II. START-UP ACTIVITY

Know them first:
Before we start let’s have a quick prior knowledge on the terms that we will encounter in this topic.
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Look/search and read for the definition of the following terms below:

PRIOR KNOWLEDGE: Definition of Terms

1. Precambrian - being the earliest period of geologic history, or the corresponding system of rocks,
which is defined by the arrival of single-celled creatures and is equal to the Archean and
Proterozoic eons.
2. Paleozoic - is the earliest of three geologic eras of the Phanerozoic Eon.
3. Mesozoic - also called the Age of Reptiles and the Age of Conifers, is the second-to-last era of
Earth's geological history, lasting from about 252 to 66 million years ago and comprising the
Triassic, Jurassic and Cretaceous periods.
4. Cenozoic - is Earth's current geological era, representing the last 66 million years of Earth's
history.
5. Epoch – it is the date and time that a computer's clock and timestamp values are calculated
against.
6. Cambrian - was the first geological period of the Paleozoic Era, and of the Phanerozoic Eon.
7. Ordovician - is a geologic period and system, the second of six periods of the Paleozoic Era.
8. Silurian - between the Ordovician and Devonian periods, this is the third epoch of the Paleozoic
era.
9. Devonian - between the Silurian and Carboniferous periods, there was a fourth epoch in the
Paleozoic era.
10. Carboniferous - is a Paleozoic geologic epoch and system that stretches 60 million years from the
end of the Devonian Period (358.9 Mya) to the start of the Permian Period (298.9 Mya).
11. Permian - between the Carboniferous and Triassic periods, this is the last period of the Paleozoic
era.
12. Triassic - is the first and shortest period of the Mesozoic Era.
13. Jurassic - is a geologic epoch and stratigraphic system that lasted around 145 million years from
the end of the Triassic period (201.3 million years ago) to the start of the Cretaceous period (201.3
million years ago).
14. Cretaceous - it is the longest geological period of the entire Phanerozoic.

PRE-ACTIVITY:
1. What is the age of the Earth?
- 4.543 billion years

2. What was the Earth like million years ago? Describe.

- The Earth was incapable of supporting life. The atmosphere was devoid of oxygen, and the Earth's surface
was scorching hot. The Earth gradually transformed over millions of years, allowing plants and animals to
begin to grow. The Earth was then further altered by living organisms.

3. Watch a video clip on YouTube. Geological Time Scale and Fossils (https://www.youtube.com/watch?
v=3EfewdEC8bk)

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 https://clarkscience8.weebly.com/geologic-time-scale.html

III. TOPIC CONTENT

The Geological Time Scale (GTS)

A. Four eras - Precambrian; Paleozoic; Mesozoic; Cenozoic
B. Periods under the Paleozoic era - Cambrian, Ordovician, Silurian, Devonian, Carboniferous, Permian
C. Periods under the Mesozoic era - Triassic, Jurassic, Cretaceous
D. Periods under the Cenozoic era - Tertiary and Quaternary

CAMBRIAN EXPLOSION is the belief that there was a sudden, apparent explosion of diversity in life forms about
545 million years ago. The explosion created the complexity of multi-celled organisms in a relatively short time frame
of 5 to 10 million years. This explosion also created most of the major extant animal groups today.

TYPES OF FOSSILS DESCRIPTION EXAMPLES

Molds Impression made in a substrate = negative Shells
image of an organism
Casts When a mold is filled in Bones and teeth
Petrified Organic material is converted into stone Petrified trees; Coal balls (fossilized plants
and their tissues, in round ball shape)

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 Original Remains Preserved wholly (frozen in ice, trapped in tar Woolly mammoth; Amber from the Baltic
pits, dried/ dessicated inside caves in arid Sea region
regions or encased in amber/ fossilized resin)
Carbon Film Carbon impression in sedimentary rocks Leaf impression on the rock
Trace/ Ichnofossils Record the movements and behaviors of the Trackways, toothmarks, gizzard rocks,
organism coprolites (fossilized dungs), burrows and
nests

THE SIX WAYS OF FOSSILIZATION

1. Unaltered preservation - Small organism or part
trapped in amber, hardened plant sap
2. Permineralization/ Petrification - The organic
contents of bone and wood are replaced with silica,
calcite or pyrite, forming a rock-like fossil
3. Replacement - hard parts are dissolved and
replaced by other minerals, like calcite, silica, pyrite,
or iron
4. Carbonization or Coalification - The other
elements are removed and only the carbon remained
5. Recrystalization - Hard parts are converted to
more stable minerals or small crystals turn into larger
crystals
6. Authigenic preservation - Molds and casts are
formed after most of the organism have been
7. Destroyed or dissolved

DATING FOSSILS
Knowing the age of a fossil can help a scientist establish its position in the geologic time scale and find its
relationship with the other fossils. There are two ways to measure the age of a fossil: relative dating and absolute
dating.
1. RELATIVE DATING
• Based upon the study of layer of rocks
• Does not tell the exact age: only compare fossils as older or younger, depends on their position in rock layer
• Fossils in the uppermost rock layer/ strata are younger while those in the lowermost deposition are oldest
How Relative Age is Determined
• Law of Superposition: if a layer of rock is undisturbed, the fossils found on upper layers are younger than
those found in lower layers of rocks
• However, because the Earth is active, rocks move and may disturb the layer making this process not highly
accurate Rules of Relative Dating
(From: http://staff.harrisonburg.k12.va.us/~esutliff/forms/Relative_Dating_1334236393.ppt)

A. LAW OF SUPERPOSITION: Sedimentary layers are deposited in a specific time- youngest rocks on top,
oldest rocks at the bottom

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B. LAW OF ORIGINAL HORIZONTALITY: Deposition of rocks happen horizontally- tilting, folding or
breaking happened recently

C. LAW OF CROSS-CUTTING RELATIONSHIPS: If an igneous intrusion or a fault cuts through existing

rocks, the intrusion/fault is YOUNGER than the rock it cuts through INDEX FOSSILS (guide fossils/
indicator fossils/ zone fossils): fossils from short-lived organisms that lived in many places; used to define and
identify geologic periods

D. IDEA OF UNCONFORMITIES: It is the contact between sedimentary rocks that are significantly different
in age or between sedimentary rocks and older, eroded igneous or metamorphic rocks.
Unconformities happen for two reasons:
Sediment deposition stopped for a considerable time and/ or existing rocks were eroded prior to being covered
by younger sediment. There is no single time span represented by an unconformity. It depends on how long
erosion occurred or for how long deposition ceased.

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2. ABSOLUTE DATING
• Determines the actual age of the fossil
• Through radiometric dating, using radioactive isotopes carbon-14 and potassium-40
• Considers the half-life or the time it takes for half of the atoms of the radioactive element to decay
• The decay products of radioactive isotopes of stable atoms.

ABSOLUTE DATING - method of measuring the absolute age of an event or object

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 Geologists often need to know the age of material that they find. They use absolute dating methods,
sometimes called numerical dating, to give rocks an actual date, or date range, in number of years. This is different
to relative dating, which only puts geological events in time order.
Isotopes are atoms of the same element that have similar number of protons but different numbers of neutrons. Most
isotopes are stable in that they stay in their original form. Other isotopes are unstable, in that they break down into
stable isotopes or other elements. They are called radioactive.

RECOMMENDED READINGS:
1.https://flexbooks.ck12.org/cbook/ck-12-middle-school-life-science2.0/section/4.13/primary/lesson/timeline-of-evolution-ms-ls/
2.https://flexbooks.ck12.org/cbook/ck-12-middle-school-earth-science-flexbook2.0/section/15.7/primary/lesson/geologic-time-scale-ms-es/
3.https://www.ck12.org/book/ck-12-earth-science-concepts-for-high-school/section/10.7/

IV. ACTIVITY EXCERCISE

MULTIPLE CHOICE. Choose the letter of the correct answer on the space provided before the number.

B. 1. The movie “Jurassic Park” got its title from which era?
A. Paleozoic B. Mesozoic C. Cenozoic D. Holozoic
A. 2. The Mesozoic Era was the Age of Reptiles while the current Cenozoic Era is the Age of
A. Mammals B. Birds C. Humans D. Technology
B. 3. The era of middle life, a time of many changes on Earth
A. Paleozoic B. Mesozoic C. Cenozoic D. Holozoic
A. 4. The largest division of the geologic time scale is the
A. Eon B. Era C. Period D. Epoch
A. 5. During which era were the first land plants formed?
A. Cambrian B. Pre-Cambrian C. Paleozoic D. Mesozoic
B. 6. Which geologic event occurred during the Mesozoic era?
A. Pangaea formed B. Asteroids killed the dinosaurs
C. The Rocky Mountains formed D. The Pleistocene Ice Age began
A. 7. What is the longest part of Earth’s history where trace fossils appeared.
A. Pre-Cambrian B. Paloezoic C. Mesozoic D. Cenozoic
C. 8. The layers in sedimentary rocks are also called
A. eras B. epochs C. strata D. gaps
A. 9. The end of this era was believed to be caused by a comet or asteroid colliding with Earth, causing a huge
cloud of dust and smoke to rise into the atmosphere, blocking out the sun.
A. Paleozoic B. Holozoic C. Mesozoic D. Cenozoic
D. 10. The geologic time scale is subdivided into 4 groups. List them from the largest to the smallest.
A. Eons, periods, epochs, eras B. Eras, eons, periods, epochs
C. Epochs, periods, eras, eons D. Eons, eras, periods, epochs

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 LESSON 4
MECHANISMS THAT PRODUCE CHANGE IN POPULATIONS

I. INTRODUCTION
Before we start let’s have a quick prior knowledge on the terms that we will encounter in this topic.
Look/search and read for the definition of the following terms below:

PRIOR KNOWLEDGE: Definition of Terms

1. Natural Selection - is the difference in individual survival and reproduction caused by phenotype
differences.

2. Genetic Variation - is the difference in DNA among individuals or the differences between population.

3. Mitigation - is the process of reducing something toxic or its adverse effects.

4. DNA Sequence - the method of determining the nucleic acid sequence - the order of nucleotides in DNA
– is known as nucleotide sequencing. Any method or technology for determining the order of the four bases:
adenine, guanine, cytosine, and thymine is included.

5. Mutation - is a change in the nucleotide sequence of an organism's genome, virus genome, or

extrachromosomal DNA.

6. Genetic Drift - is the change in the frequency of an existing gene variant in a population due to random
sampling of organisms.

7. Genotype - it describes an organism's entire set of genes and relates to the genetic makeup of that
creature. In a more restricted meaning, the phrase can refer to the alleles, or alternative forms of a gene, that
an organism carries.

8. Genetic Equilibrium - is a state in which the frequency of an allele or genotype in a gene pool does not
change from generation to generation. It describes a theoretical condition that serves as the foundation for
determining if and how populations might stray from it.

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HARDY–WEINBERG LAW

The law that states that in an infinitely large, interbreeding population in which mating is random and in
which there is no selection, migration, or mutation, gene and genotype frequencies will remain constant from
generation to generation. In practice these conditions are rarely strictly present, but unless any departure is a marked
one, there is no statistically significant movement away from equilibrium. Consider a single pair of alleles, A and a,
present in a diploid population with frequencies of p and q respectively. Three genotypes are possible, AA, Aa, and aa,
and these will be present with frequencies of p2, 2pq, and q2 respectively.
https://www.encyclopedia.com/science-and-technology/biology-and-genetics/genetics-and geneticengineering/hardyweinberglaw#:~:text=Hardy
%E2%80%93Weinberg%20law%20The%20law,generation%2C%20with%20no%20overlap%20between

II. START-UP ACTIVITY

PRE-ACTIVITY: We are one but not the same

1. Observe the two pictures and in the table below write five (5) the similarities and differences between
individuals and animals belonging to the same species.

SIMILARITIES DIFFERENCES
HUMANS 1. 1.
2. 2.
3. 3.
4. 4.
5. 5.
ANIMALS 1. 1.
2. 2.
3. 3.
4. 4.
5. 5.

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The five (5) conditions that must be met for genetic equilibrium to occur include:
1. No mutation (change) in the DNA sequence.
2. No migration (moving into or out of a population).
3. A very large population size.
4. Random mating.
5. No natural selection.
https://www.ck12.org/book/ck-12-life-science-concepts-for-middle-school/section/4.9/

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III. TOPIC CONTENT

HARDY-WEINBERG EQUATION
A mathematical equation that can be used to calculate the genetic variation of a population at equilibrium. The
equation is an expression of the principle known as Hardy-Weinberg equilibrium, which states that the amount of
genetic variation in a population will remain constant from one generation to the next in the absence of disturbing
factors. p2 + 2pq + q2 = 1 where p is the frequency of the "A" allele and q is the frequency of the "a" allele in the
population. In the equation, p2 represents the frequency of the homozygous genotype AA, q2 represents the frequency
of the homozygous genotype aa, and 2pq represents the frequency of the heterozygous genotype Aa. In addition, the
sum of the allele frequencies for all the alleles at the locus must be 1, so p + q = 1. If the p and q allele frequencies are
known, then the frequencies of the three genotypes may be calculated using the Hardy-Weinberg equation.
https://www.nature.com/scitable/definition/hardy-weinberg-equation-299/#:~:text=Science%20at%20Scitable-,Hardy%2DWeinberg%20equation,In
%201908%2C%20G.%20H.&text=If%20the%20p%20and%20q,using%20the%20Hardy%2DWeinberg%20equation

NATURAL SELECTION, GENETIC DRIFT, AND GENE FLOW

Mechanisms that cause changes in allele frequencies over time. When one or more of these forces are acting
in a population, the population violates the Hardy-Weinberg assumptions, and evolution occurs.
Natural selection occurs when individuals with certain genotypes are more likely than individuals with other
genotypes to survive and reproduce, and thus to pass on their alleles to the next generation. As Charles Darwin (1859)
argued in On the Origin of Species, if the following conditions are met, natural selection must occur:
1. There is variation among individuals within a population in some trait.
2. This variation is heritable (i.e., there is a genetic basis to the variation, such that offspring tend to resemble
their parents in this trait).
3. Variation in this trait is associated with variation in fitness (the average net reproduction of individuals with
a given genotype relative to that of individuals with other genotypes).

MUTATION
Although mutation is the original source
of all genetic variation, mutation rate for
most organisms is pretty low. So, the
impact of brand-new mutations on allele
frequencies from one generation to the
next is usually not large. (However,
natural selection acting on the results of a
mutation can be a powerful mechanism
of evolution!)

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NATURAL SELECTION
Finally, the most famous
mechanism of evolution! Natural
selection occurs when one allele (or
combination of alleles of different
genes) makes an organism more or
less fit, that is, able to survive and
reproduce in a given environment. If
an allele reduces fitness, its
frequency will tend to drop from one
generation to the next. We will look
in detail at different forms of natural
selection that occur in populations.

GENE FLOW
Gene flow involves the movement of genes
into or out of a population, due to either the
movement of individual organisms or their
gametes (eggs and sperm, e.g., through pollen
dispersal by a plant). Organisms and gametes
that enter a population may have new alleles,
or may bring in existing alleles but in different
proportions than those already in the
population. Gene flow can be a strong agent of
evolution.

GENETIC DRIFT
Non-infinite population size (genetic
drift). Genetic drift involves changes in allele
frequency due to chance events – literally,
"sampling error" in selecting alleles for the
next generation. Drift can occur in any
population of non-infinite size, but it has a
stronger effect on small populations. We will
look in detail at genetic drift and the effects of
population size.

https://www.khanacademy.org/science/biology/her/heredity-and-genetics/a/hardy-weinberg-mechanisms-of-evolution
IV. ACTIVITY EXCERCISE
How do you think the following items below affect the number of populations in the environment?

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  ARTIFICIAL SELECTION
It permits individuals with various genetically determined features to have different reproductive
success in order to enhance the frequency of desirable traits in the community.
 NATURAL SELECTION
It may result in microevolution, with fitness-enhancing genes becoming more common in the population.

 GENETIC DRIFT
It can result in the extinction of rare alleles and a shrinking of the gene pool. Genetic drift can also
cause a large population to diverge genetically from its ancestral population, leading to the hypothesis
that genetic drift plays a role in the development of new species.
 GENE FLOW
It can increase genetic variety, but it can also reduce genetic divergence between genetically
dissimilar populations.

 MUTATION
It has the ability to introduce new alleles into a community of organisms, increasing genetic
variety.
 RECOMBINATION
It raises a population's genetic burden under stabilizing selection. Because it breaks up beneficial
allele combinations, it should result in a decrease in mean fitness.

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