General
In the transformation process, a selected
Biology 2
Genetic Engineering
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:
I. introduction of new traits into an
organism
II. enhancement of a present trait by
increasing the expression of the desired
gene
III. enhancement of a present trait by
disrupting the inhibition of the desired
genes’ expression.
Example:
 Wagyu Beef (Beef with good fat
 distribution)
 Guapple (Large sized guava)
 Human Insulin-producing bacteria
 Flavr-Savr (Delayed-ripening
tomatoes)
 Macapuno trait in coconuts
It is a process of making changes on the
genetic code of an organism.
Its goal is to add one or more new traits
that are not normally found in that
organism.
DNA Recombination is a process of
modifying the genes of organisms for
practical purposes.
It is done when a piece of DNA is combined
with another DNA from another source.
The resulting genetic product is called
recombinant DNA.
Processes Used in Recombinant DNA
Technology
Transformation Using a Vector
VECTORS are organisms that are normally
harmless but may help spread infection by
transferring the genetic material from one
host to another.
portion of the foreign DNA is inserted into a
small, circular DNA molecule called
PLASMID, which is naturally found in
bacteria.
Plasmid is the most useful tool in gene
transformation.
A plasmid contains a gene sequence that
serves as a bacterial ORIGIN OF
REPLICATION. This is where the foreign
DNA can be inserted into the bacterial cell.
It also contains a GENETIC MARKER,
which makes it possible to distinguish
bacteria that carry the plasmid-containing
foreign DNA. Some of these genetic
markers code for antibiotic resistance.
A genetic marker is a gene or DNA
sequence with a known location on a
chromosome that can be used to identify
individuals or species.
During transformation, a RESTRICTION
ENDONUCLEASE ENZYME is used to
cut the piece of the donor DNA. This
enzyme cleaves the DNA at the phosphate-
sugar bond, and thus sticky ends are
created.
Not all restriction enzymes produce sticky
ends. Some are “blunt cutters,” which cut
straight down the middle of a target
sequence and leave no overhang.
Example: SmaI enzyme
Restriction enzymes cut the DNA only at a
specific nucleotide sequence.
Then, an enzyme known as DNA ligase is
used to insert the donor DNA into the
vector. It seals the sticky ends by joining the
phosphate and the sugar bonds in the DNA.
The inserted DNA also contains a genetic
marker for identification.
Ligase’s job is to join together fragments
of newly synthesized DNA to form a
seamless strand. 
The process of attaching fragments of DNA
from different sources is known as gene
splicing.

Vectorless Gene Transfer
This process is similar to transformation,
but it does not involve vectors.
The types of vectorless gene transfer include
electroporation, protoplast fusion,
microinjection, and use of a particle gun.
Pseudomonas syringae-
the recombinant variant of this bacterium is
the ice-minus bacterium, which lacks the
gene responsible for ice formation. The ice-
minus bacteria prevent frost crystals from
forming in plants.

In ELECTROPORATION, temporary Pseudomonas fluorescens-

holes are formed in the plasma membrane of
the host cell by applying a significant
amount of electricity in the culture medium.
This enables the entry of foreign DNA via
the pores.
In PROTOPLAST FUSION, cells are
treated with chemicals to initiate
recombination. In this process, bacterial
cell walls are digested, turning the cells
into protoplasts.
Protoplast (from 'first-formed'), is a
biological term coined by Hanstein in 1880
to refer to the entire cell, excluding the cell
wall.
These protoplasts are treated with
polyethylene glycol to allow them to fuse,
creating a random recombination of genes.
The resulting recombinant cell will now
grow a new cell wall.
In MICROINJECTION, the host cell is
immobilized by applying a mild suction
with a blunt pipette. The foreign gene is
then injected with a microinjection needle,
thus creating recombinant DNA.
this is a nonpathogenic bacterium that has
the ability to produce proteins rapidly. This
characteristic is advantageous in developing
biotherapeutics and vaccines.
Agrobacterium tumefaciens-
in its natural state, this bacterium has a
tumor inducing (Ti) plasmid that causes
CROWN GALL DISEASE (the formation
of tumors) in plants. The said Ti plasmid in
the bacterium can be removed and replaced
with a recombinant plasmid. This enables
the now-modified bacterium to introduce
beneficial genes to plants.
Geological Time Scale
The Geological Time Scale is a record of
the life forms and geological events in
Earth’s history.

In using a PARTICLE GUN for

recombination, the host cell is bombarded
with tungsten particles coated with foreign
DNA. Many farmers use this method to
genetically modify plants to make them
highly resistant to insects and other pests.

Transduction
It is the process wherein genetically
engineered BACTERIOPHAGES- viruses
that parasitize bacteria- are introduced into
the cell to create the desired recombinant
DNA.

TRANSGENIC PLANTS- plants that

contain genes from other organisms, are
now an important part in the field of
agriculture.
Divisions of Geologic Time
Eras are subdivided into periods. Periods are
subdivided into epochs. Precambrian Era
covers approximately 88% of Earth’s
History.
One Super Eon and Four Eras
Pre-Cambrian Super Eon- 88% of Earth’s
history
Paleozoic (ancient life)- 544 million years
ago… lasted 300 million years
Mesozoic (middle life)- 245 million years
ago… lasted 180 million years
Cenozoic (recent life)- 65 million years
ago… continues through present day
PALEOZOIC ERA (Ancient Life)
The Cambrian period is the 1st period of the
Paleozoic Era. “Age of the Trilobites” or
the “Age of Fish”
Explosion of life in the oceans began during
this era
MESOZOIC ERA (Middle Life)
At the beginning of this era, the continents
were joined as Pangaea.
Pangaea broke up around the middle of this
era.
Reptiles became the most abundant animals
because of their ability to adapt to the drier
climate of the Mesozoic era.
Dinosaurs were very active in this era.
Small mammals and birds appeared during
this era.
This era ended with a mass extinction
event about 65 million years ago.
CENOZOIC ERA
Growth of these mountains may have helped
to cool down the climate.
As the climate changed, the animals had to
adapt to the rise and fall of the oceans
caused by melting glaciers.
This era is sometimes called the “Age of
Mammals.”
GENETIC VARIATION
The differences between the genes of each
individual and the differences between genes of
the different populations are termed as
GENETIC VARIATION.
The number of times at which the common
gene appears in everyone within a
population is called GENE FREQUENCY.
Any change in the gene frequency of a
species or population is EVOLUTION.
MECHANISMS OF EVOLUTION
1. Artificial Selection- This is also termed
as selective breeding. One of the causes of
change in the gene frequency of some
species specifically domesticated plants and
animals is artificial selection or selective
breeding. It is when humans selectively
choose to breed animals and plants with
specific traits that they deemed beneficial
for different purposes.
2. Natural Selection- Nature or the
environment dictates which among the
organism will survive, this organism has a
certain variety of traits or characteristics that
will be passed on to the next generation.
-also known as “Survival of the fittest”
3. Gene Flow or Migration- Another
mechanism of evolution is gene flow or
migration. This occurs when a group or
individual specie migrated from one place to
another affecting the gene pool of the place
that they left and the place where they
arrive.
4. Genetic Drift- is a mechanism that may
bring change to the gene frequency in a
population because of “chance” events. It is
a result of an incident or accident which
may have brought significant and palpable
change to the gene frequency or common
traits in a given population.
An event that significantly reduces the
number of populations is called the
Bottleneck Effect.
5. Non-Random Mating- It occurs when
some species choose a partner with
preferred characteristics. Some female
species only allow certain male
characteristics to be their partner, making
the genes of the chosen male species to
reproduce in the next generation.
The principle of lateral continuity states that
layers of sediment initially extend laterally
in all directions; in other words, they are
laterally continuous.
Unconformity

6. Recombination- Recombination or gene Unconformities are disturbance in the rock

shuffling is life’s way of bringing variety in
similarity. It occurs during meiosis, the cell
replication process used for reproduction.
Recombination is also the reason behind
gene variation between siblings and twins
and makes genetic diversity possible.
7. Mutation- A Mutation occurs when an
insertion, deletion, or any change in the
codes of the DNA takes place. Changes in
the DNA codes may result from internal or
external factors.
layers. Not all rock layers are in nice and
neat straight rows. Many have features that
cut through them.
Disconformity
Disconformities are unconformities that
occur between parallel layers of strata
indicating either a period of no deposition or
erosion.
Paraconformity

Relative and Absolute Dating A type of unconformity (gap in the geologic

system) in which there is no evidence of a
gap in time, because the planes above and
Relative Dating- The process of
below the gap are parallel and there is no
determining whether an object or event is
evidence of erosion.
older or younger than any other object or
events. It puts object/ events in
A Geologic Column is an ordered
chronological order.it does not indicate the
arrangement of rock layers that is based on
rock’s year in age.
the relative ages of the rocks, with the oldest
rocks at the bottom.
Inclusion- Inclusions are pieces of rocks
contained within another. In the same way,
Index Fossils
anything (mineral ,etc.) that is enclosed/
embedded. In the rock are older than the
1. Wide geographic abundance,
rock unit surrounding unit.
2. Easy identification,
3. And a relatively short geological
The Principle of Superposition
existence.
Younger rock lies above older rocks in
Absolute Dating- Measuring the age of an
undisturbed sequences.
event or object in years using radioactive
isotope.
The Principle of Crosscutting
Relationship
Radiometric Dating
The principle of crosscutting relationships
Method of finding out the age of an object
states that geological features such as faults
by figuring our the ratio of parent material
and intrusions are younger than the rock
to daughter material.
they cut through.

Law of Lateral Continuity

Radioactive Decay
 Cladograms
To determine absolute age, scientists look at
the breaking down of an unstable isotope
CLADE (also known as a monophyletic
into a stable isotope.
group or natural group), is a grouping of
organisms that are composed of a common
Isotope
ancestor and all its lineal descendants – on a
An atom that has a different number of
phylogenetic tree.
neutrons than other atoms of the same
element.
The key difference between ingroup and
outgroup in biology is that an ingroup is a
Half Life
group of closely related taxa that is
investigated for evolutionary relationships
The amount of time it takes for half of the
while outgroup is a reference group or a
radioactive sample to decay.
taxon outside the group of interest and more
distantly related to the ingroup.
The Development of Evolutionary
Thoughts
A root is the ancestral population from
which all the other species originate. A node
1. Jean Baptiste Lamarck
represents a branching point from the
Before Darwin, some notable people who
ancestral population.
have already thought about the concept of
evolution. One of them is Jean Lamarck, a
The nodes represent biological entities (e.g.,
French Naturalist who has theorized on
species, genes), whereas the branches
habits or the Principle of Use and Disuse;
represent relationships between those
he thought that organisms have evolved to
entities (e.g., ancestor-descendant
change their characteristics to fit in their
relationships).
environment through continuous use and
disuse of their organs.
Internal branches or internodes connect two
nodes, whereas external branches connect a
2. Charles Darwin
tip and a node.
Darwin, an English Naturalist, as we have
already learned, had theorized on how
The Taxa is known as the "tips" of the tree
species came from a common ancestor and
branches or the study being conducted.
how these species may also give birth to
another species in a long time as changes
Cladograms is used to illustrate
occur in their characteristics via the process
relationships among organisms and
of Natural Selection. These organisms
evolutionary relationships for organisms
change to adapt to their environment as time
with a shared common ancestor.
passed by until they have finally evolved
into a new species incapable of breeding
An out-group is the organism in a
with the original species.
cladogram that is the starting point and
usually does not have any common
3. Alfred Russel Wallace
characteristics with the other organisms in
He is a British Naturalist, had been a friend
the cladogram.
of Darwin, and is of great significance to the
development of evolutionary thought
because he had been a key person to
Darwin’s Publication of the Origin of
Species.