General Biology 2

Process of Genetic Engineering

TOPIC: Genetic Engineering
Genetic Engineering 1. DNA Isolation
- A process of making changes on the opposite code 2. Ligation
of an organism. 3. Transformation
- It is to add one or more traits that are not normally 4. Cloning
found in that organism’s DNA structure.
5. Selection
- It is also called as Genetic modification.
6. Infection
Genetic modification is the manipulation of:
1. TRANSGENIC – a gene is moved from Step 1: DNA Isolation
one non-closely related species to
another. - Plasmid is an extra chromosomal circular DNA
2. CISGENIC/INTRAGENIC – moved within strand in the bacterium’s cytoplasm
the same species or a closely related - Gene of interest - “target gene” often just
species. means “gene of interest”, or the particular gene
3. SUBGENIC – insert being studied or manipulated in an experiment.
DNA Recombination
- A process of modifying the genes of organism for Step 2: Ligation
practical purposes.
- Restriction enzymes – also known as DNA –
- A piece of DNA is combined with other DNA.
main role is to cleave DNA into fragments on
Recombinant DNA – the resulting genetic product. specific recognition sites.
Recombinant DNA Technology – a technique that
- DNA ligase – DNA joining enzyme because its
combines DNA sequences. main role is to ligate or join two DNA standards.

Genetically modified maize – a genetically modified crop Step 3: Transformation

and
Genetically modified bacteria – (cyanobacteria) E-Coli =
one important GM bacterium.
History of Recombination DNA Technology
Stewert Linn and Werner Arber discovered
restriction enzymes in E-Coli (Escherichia Coli)
known as Endonucleases.
Genetically Modified Organisms
- Genomes that were engineered in the
laboratory.
Artificial Selection in Brassica
- A natural process where bacteria can take up
the genetic material in the environment.
- Process can also be done in vitro
Step 4: Cloning
- If the bacteria host cell ingests a plasmid, they
are called transformed cells, which maybe
either recombinant or non-recombinant.
Recombinant cells – with the gene of interest.
Non-Recombinant cells – without gene of interest.
Non-transformed cells – did not take up any plasmid.

1. Cabbage Selection for terminal buds. Step 5: Selection

2. Brussel Selection for lateral buds. - A medium containing x-gal is used to select
sprouts
transformed cells that take up the recombinant
3. Kohlrabi Selection for stem.
4. Kale Selection for leaves. plasmid. Here, the white colonies (small circles)
5. Broccoli Selection for stems and flowers. are desired cells.
6. Cauliflower Selection for flower clusters.
Step 6: Selection
- Plant will grow and be transformed into a plant
resistant.

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 Increased productivity Decreased pesticide
Transgenic Organism effectivity.
Cheaper
TOPIC:medicine
Evolution High
and thecost for GM
Origin of seeds
life
- Organisms such as bacteria, plants, and animals
can be genetically modified. Once they are modified
Cellular complexity
they are now called transgenic organisms.
Genetically modified bacteria – (cyanobacteria) - All living things are composed of either one or more
- E-Coli = one important GM bacterium. cells that are highly complex yet organized and
- This kind of bacterium is genetically modified to enclosed with membranes.
produce a synthetic human insulin. Also, E-coli
bacteria have been modified to produce disease Growth and development
fuel. - Living things use energy to grow by metabolizing by
BT CORN cellular respiration or photosynthesis.
- Is a pest resistant plant that is dangerous to - Organism also undergo different life stages.
pest but not to humans.
Reproduction
BANANA VACCINE
- An engineered banana to become an edible - Continuity of life would definitely be impossible
vaccine against hepatitis virus. without reproduction.
GOLDEN RICE
Irritability
- Produces high amounts of beta carotene which
is helpful to fight not only malnutrition but also - All organisms are sensitive to different stimuli – may
some eye-related problems such as blindness. it be environmental or physiological.
- This may refer to any form of response or
Advantages of Genetically modified movement to stimuli in its own violation. (Dubeck et
plants al., 2004)
- response to stimuli
Herbicide tolerance Homeostasis
- Crop can withstand herbicide applications.
Insect tolerance - Living things maintain relatively constant internal
- Plants produces toxin to kill pest. conditions which are different from their
environment.
Improved nutrition
- Plant produces a substance of nutritive value or Geologic Time Scale of the Earth’s History
is changed to not produce anti-nutrient.
Disease resistant
- A crop is resistant to certain disease. Ca 4.6-3.8 billion years ago
Stress tolerance - Formation Earth’s crust and oceans
- A crop is resistant of stress, low nutrient levels
of excess nutrients. Ca 3.5 billion years ago
Increased storage - Oldest Geological evidence of life
- A crop can be stored longer to avoid spoilage
Ca 3 billion years ago
losses.
Medicinal uses - Propagation of Cyanobacteria
- Crops that produce medicines or vaccines. Ca 2 billion years ago
Industrial uses
- Appearance of first Eukaryotes
- Crops to make more efficient industries.
Ca 1.2 billion years ago
Benefits and Risks of Genetic Engineering
- Influx of Multicellular organisms
BENEFITS RISKS
Ca 500 million years ago
Improved nutrition Reduced biodiversity
Disease detection Allergic reactions - The Cambrian explosion

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 Ca 200 million years ago
- Arrival of modern human Spontaneous Generation

TOPIC: Theories about Origin of A superseded scientific theory that

Life held that living creatures could arise
from nonliving matter and that such
processes were commonplace and
Panspermia & Abiogenesis regular.

Panspermia Originators of Spontaneous Generation

Anaxagoras (5th Century BC) 1. Pier Antonio Micheli

A hypothesis that depicts life exist 2. Francisco Redi
throughout the universe, conveyed by 3. Aristotle
space dust, meteoroids, asteroids, 4. John Needham
comets, and planetoids, as well as by 5. Lazzaro Spallanzani
spacecraft carrying unintended 6. Louis Pasteur
contamination by microorganisms. 7. John Tyndall
An atmosphere full of reduced gas Pier Antonio Micheli
molecules and a source of energy
needed to convert these molecules An Italian botanist, performed another
into important biological precursors experiment in 1729 where he placed
required for life. fungal spores on a slice of melon and
An ocean that is teeming with observed that the same was produced
biological molecules. on the melon slice.
A process to produce from this ocean Francisco Redi
of molecules the kinds of information-
rich polymers essential for a living cell. Franceso Redi was an Italian naturalist
A belief that if step 3 can be executed, who challenged the ancient belief of
it will result almost inevitably to the spontaneous generation of maggots
creation of a living cell. on decaying meat in 1668.

Abiogenesis
Thomas Henry Huxley (late 19th
century)
The natural process by which life has
arisen from non-living matter, such as
simple organic compounds.
Models of Abiogenesis
Aristotle
Aristotle theorized that non-living
matter contained a “vital heat” called
pneuma—the concept of a “breath of
life” and translated later as “anima”
meaning “soul” in Latin—and a
combination of the four elements
believed to make up all life: earth, air,
fire and water.

1. Spontaneous Generation John Needham

2. "Primordial Soup" Theory He infused a broth by mixing plant and

animal matter and boiled it in the belief
3. The Clay Hypothesis that it would kill all the
4. Deep Hot Biosphere Hypothesis microorganisms.

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Lazzaro Spallanzani
According to his observations, the
sealed jar was clear and did not have
any growth. He then concluded that air
was the force that was introducing
microbes into the flask.
Louis Pasteur
A French Microbiologist, conducted
another broth experiment that settled
the question of spontaneous
generation once and for all.
John Tyndall
An Irish Physicist, advanced the work
of Louis Pasteur and finally the theory
of spontaneous generation was
disproved.
“Primordial Soup” Theory
The theory states that if energy is
added to the gases that made up
Earth's early atmosphere, the building
blocks of life would be created.
THE OPARIN-HALDANE THEORY
Both believed that organic molecules
could be formed from Abiogenic
Materials in the presence of an
external energy source (e.g., ultraviolet
radiation) and that the primitive
atmosphere was reducing (having very
low amounts of free oxygen) and
contained ammonia and water vapour,
among other gases.
THE MILLER-UREY EXPERIMENT
The two scientists combined water
with a mixture of four gases —
WATER VAPOUR, methane,
ammonia, and molecular hydrogen—
and pulsed the “atmosphere” with
electrical discharges
One week later Urey and Miller found
that simple organic molecules,
including amino acids (the building
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blocks of proteins), had formed under
the simulated conditions of early Earth.
The Clay Hypothesis
The microstructure of clay is formed
by an irregular crystal, in which the
individual series of silicate molecules
lie above one another in regularly
ordered layers.
The hypothesis also in no way
resolves the problem of the evolution
of the genetic code and
proteosynthetic apparatus.
GRAHAM CAIRNS-SMITH
He based the concept on the original
structure that provided for transfer of
information that could have been a
clay-type inorganic substance rather
than an organic compound
The Deep Hot Biosphere Hypothesis
The first indications of deep life came
from studies of oil fields in the 1920s,
but it was not certain that the
organisms were indigenous until
methods were developed in the 1980s
to prevent contamination from the
surface.
Gold believes it has been there since
the earth's formation, that it supports
its own ecosystem far underground
and that life there preceded life on the
earth's surface.
THOMAS GOLD
A vast diversity of uncultivated
microorganisms has been detected in
subsurface environments, and we
show that H2, CH4, and CO feature
prominently in many of their predicted
metabolisms.
TOPIC: Key Proponents and Developers
of the Concept of Evolution
1. Jean Baptiste de Lamarck
 2. Charles Darwin
3. Alfred Russel Wallace
4. Gregor Johann Mendel
Jean Baptiste de Lamarck (1744-1829)
A French scientist whose one of the
first proponent of the idea of evolution.
LAMARCK'S THEORY OF ADAPTATION
He proposed that if an animal could
develop a particular characteristic in its
lifetime, the straight could be passed
on to their offspring and its succeeding
generations.
He cited as an example the long neck
of giraffe.
This particular trait is developed and
passed on to the next generation.
Most scientist during that time thought
that Lamarck was silly and only a few
radical thinkers believe in the concept
of single origin and changes in
species.
Charles Darwin (1809-1882)
an English naturalist and geological
developed his theory about evolution.
NATURAL SELECTION
His expedition around the world from
1831-1836 on HMS Beagle as a young
naturalist enabled him to study
different specimens around the globe.
If an organisms developed and
possessed a small inherited variation
that would increase the individual’s
ability to compete, survive, and
reproduce, this characteristic will pass
on to the next generation.
In 1859, he published the idea of his
Origin of Species by Means of
natural Selection.
Alfred Russel Wallace
With an already accepted theory of
evolution in mind as a strong supporter
of Darwin, Alfred Russel Wallace
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started an expedition of his own in
1848 through the Amazon and
Southeast Asian region.
He wanted to demonstrate that
evolution took place by showing how
geography influenced the current
distribution of species.
Studied hundreds of thousands of
animals and plants, meticulously
recording the exact localities where he
had observed them.
DARWIN-WALACE THEORY OF
EVOLUTION BY NATURAL SELECTION
July 1, 1858 On the Tendency of
Species to form Varieties; and on the
Perpetuation of Varieties and Species
by Natural Means of Selection.
Found a pattern that corroborated the
evidences of evolution: physical
barriers (e.i., rivers or mountain
ranges) served as a demarcation of
many species distributional range.
Gregor Johann Mendel (1822-1884)
The Father of Genetics
An Austrian monk who was carrying
out imperative experiments that would
finally prove Darwin’s concept of
natural selection.
MENDEL’S KEY TO THE MISSING LINK
For seven years, Mendel cross breed
different strains of pea plants.
He did this experiment to investigate
how characteristics like the pod shape,
seed shape, or flower colors are
inherited.
He was able to cultivate almost 30,000
pea plants and in doing so figure out
the basic foundation of genetics.
He presented that an offspring can
receive characteristics from both its
parents, but the dominant traits is the
one expressed.
Mendel's work was ignored by scientist
in Britain and only in 1990 when
Mendel's work on genetics was finally
“re-discovered”.
 His experiment becomes plausible
proof to support the natural selection
idea of Darwin.
TOPIC: Evidence from Geographic
Distribution: Biogeography
“THE PENTADACTYL LIMB”
Many vertebrates have a very similar bone
structure despite their limbs looking very
different on the outside. This structure is known
as the pentadactyl (five fingered) limb. This
suggests that many vertebrates descended
from the same common ancestor.

BIOGEOGRAPHY EVIDENCE
It is the study of distribution of plants and
animals in different parts of the earth.
The way in which each of two or more things is
related to the other or
others.
Bio geographers help us determine how and
where different species migrated.
A clear pattern of how current distribution of The horse's pentadactyl leg is an example of
species offers evidence for shared ancestry how evolution has changed the way horses'
can be perceived in archipelagos. feet have developed over thousands of years.
Because they could evade predators, they had
Comparative of Anatomy an evolutionary advantage.
Horse feet have developed to be smaller over
Comparative anatomy is the study of the many generations, while horses themselves
similarities and differences in the structures of have grown bigger and stronger.
different species. Similar body parts may be
ANALOGOUS STRUCTURES
homologies or analogies. Both provide
evidence for evolution. Analogous structures are structures that are
similar in unrelated organisms. The structures
HOMOLOGOUS STRUCTURES
are similar because they evolved to do the
Homologous structures are structures that are same job, not because they were inherited from
similar in related organisms because they were a common ancestor.
inherited from a common ancestor. These
structures may or may not have the same
function in the descendants.

The picture above shows the hands of several

different mammals. They all have the same
basic pattern of bones. They inherited this
pattern from a common ancestor. However,
their forelimbs now have different functions.

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 of lesser species, such as mollusks (squids and
octopuses), do not have a blind spot because
the retina is located in front of the optic nerve.
Their ancestors may have had structures that
were already developed into working eyes that
did not require any blind spots.

Comparative Embryology

Vestigial Structures and Organs

During vertebrate development, all embryos
exactly look the same during the very early
stages of development. All vertebrate embryos
are characterized by having gill pouches and
tails. Thus, even if they will develop into
different adult stages, a reptilian embryo, an
avian embryo, and a human embryo look very
similar.
Vestigial structures are cells, tissues, and
organs in the body that no longer function or
have a significant role that highly influences the
organism's internal and external structure. A
vestigial structure can develop as a result of a
genetic mutation.

Because the structures are no longer used,

evolution has reduced their size. An example of
a vestigial structure is the human appendix. It is
a remnant of a once-larger organ. It was
required to digest food in a distant ancestor.

Contrivances Some characters that are passed

on through generation will not be “perfectly”
adapted based on evolutionary theory. Since
natural selection occurs on the genetic The human coccyx or tailbone, which is a much
variation that is presently available in a more condensed version of a bony tail
population, the “best” alternatives cannot possessed by our ancient lineages.
constantly be found.
Most of the time, existing traits are modified
(contrived) to serve a new function. For
example, thumbs of giant pandas are found to
have a modified wrist bone.
The human eye is another example of an
imperfect adaptation. The vertebrate retina is
technically "inside-out," as it is located behind
the nerves that form the optic nerves. The eyes

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 Previously adapted to help in balance and
climbing, a tail has small function for human
movement. It probably remained in a vestigial
form because
Biochemical it has some use as a point for
Evidences
muscle attachment.
TOPIC: Evidence from Physiology
and Biochemistry
Evolutionary Theory
Evolutionary theory basically means that if
certain organisms have similar characteristics,
they are considered to have been originated
from a single common ancestor.
Physiology
is a function of organs and organ systems and
how they work within the body to respond the
challenges.
Biochemistry
is a chemical process within and related to
living organisms.
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EVOLUTION FROM PHYSIOLOGY AND
BIOCHEMISTRY
Evidences based on similar biochemical
reactions
Enzymes
a biological catalyst and is almost always a
protein
similar enzymes of different animals are similar
in their chemical nature and made of action.
Cytochrome-C
Cytochrome - C
is an enzyme of respiratory chain and is found
in the mitochondria of all organisms.
measured in the number of differing amino
acids.
100 amino acids forming the primary structure
of Cytochrome-C and many higher order
organisms have 104 amino acids.
chicken and turkey, pigs, cows, and sheep
have identical sequence homology
Chimpanzees and humans also share identical
molecule
TOPIC: Evidence From
Paleontology: Fossil records
The study of fossil and sedimentary rocks is the
only way by which we can learn about the past
environments and climatic condition on Earth
and the ways by which life evolved and
diversified.
The sedimentary deposits contain fossils,
remains, or traces of animals, plants, and other
organisms from the remote past.
In Darwin’s time, the location of the rocks and
the fossils in them were believed to be related
to their actual age rocks and fossils that were
 generally in the deeper strata were assumed to antibiotic eliminates low-resistance bacteria
be older while the younger ones were those and due to natural selection, level of
found in the upper part. (singular form of strata bacterial population resistance rises in a
is “STRATUM”) very short time.
Nowadays, rocks are dated through radiometric
age dating where the most significant factor
considered to identify a rock age is the degree
of radioactive decay.
Since radioactive isotopes (unchanged by the
factors like temperature or pressure) decay in a
constant rate.

SELECTION IN HUMANS
most prevalent case is lactose intolerance.
Lactase production is found to decline in the
last 4 years of life
if modified, MCM6 Gene's difference removes
the production cutoff of lactase. this is a very
recent evolutionary adaptation

RELATIVE DATING
estimate whether an object is younger or older
than other things found at the site.
ABSOLUTE DATING
provide more specific origin dates and time
ranges, such as an age range in years.
The chronological order of the major group of
fossil record shows a succession of species
that was foreseen by evolutionary theory.
Fossil records have shown how cetacean
evolution had resulted to the loss of hind limbs
and the development or flippers.
Through the low probability of fossil
preservation and recovery, it is still not
surprising that there are still gaps in the fossil
record.
TOPIC: Evidence from Selection

ANTIBIOTIC RESISTANT
bacteria develop antibiotic resistance.
bacteria have an extremely quick life cycle.
can generate millions within 24 hours.
bacteria can quickly adapt to environmental
pressures.

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