HS BIO 002

BIOTECHNOLOGY ▪ DNA cloning vectors - carry target gene into a

host cell.
Biotechnology - A set of biological techniques
e.g. plasmid and bacteriophage
developed through basic research and now applied
to research and produce development. ▪ Host cell - a bacterial cell that allows the cloning
vector to replicate within it.
3 Main Parts of Biotechnology
▪ Modifying enzymes - introduces minor bases into
▪ Green Biotechnology: agricultural processes
DNA or RNA.
- It is a very important field of modern
e.g, DNA Ligase and Taq Polymerase.
biotechnology. It focuses on crop improvement and
production of novel products in plants, which is
achieved by implanting foreign genes to plant
species that is economically important. Methods in Gene Cloning
Stage 1: Isolation of a target gene
▪ Red biotechnology: health care processes
- traditional drug discovery and also in creating new This process can be done using:
possibilities for treatment, prevention, and diagnosis
1. Cutting the gene from a complete chromosome
(by using new methods).
using a restriction enzyme.
▪ White Biotechnology: industrial and 2. Producing a complementary DNA (cDNA).
environmental processes
- uses molds, yeasts, bacteria, and enzymes to
produce goods and services or parts of products. It Stage 2: Insertion of a target gene into a vector
offers a wide range of bio-products like detergents,
▪ Gene is inserted into vectors such as plasmids
vitamins, antibiotics, etc.
and bacteriophages resulting in Recombinant DNA.

▪ Bacterial plasmids that have been isolated from

Recombinant DNA Technology
DNA Recombination
▪ occurs randomly during Meiosis I through
crossing over of homologous chromosomes during
fertilization or through mutations or transformations.
▪ With the advent of technology and various studies
are done, DNA recombination can now be
manipulated to serve specific purposes, and this
process is known as Recombinant DNA technology.
Recombinant DNA technology
bacterial cells must be mixed with the same
restriction enzymes used to cut the DNA molecule.
This is done to produce the same sequence of
sticky ends.
▪ The exposed bases on the sticky ends will attract
the complementary bases of other sticky ends and
form hydrogen bonds.
▪ They are then joined by ligase thus producing two
types of the plasmid:
1. Does not carry the target gene due to reannealing
2. Recombinant DNA which carries the target gene.

▪ Refers to various techniques and procedures used

in gene manipulation.
▪ It involves modifying and recombining DNA's to
produce desired products such as proteins, or
animals and plants with desirable traits.
▪ It has wide-ranging applications in the fields of
medicine, forensic, pharmaceuticals, and
agriculture, especially in improving livestock and
crop production.
Stage 3: Introduction of vector into a host
▪ The plasmids carrying the target gene must be
introduced into a host cell through transformation,
and only a lesser amount will contain the
recombinant plasmid.
Stage 4: Amplification of the target gene by the
host cell (cloning) ad screening

▪ Following the introduction of the recombinant

Tools used in Recombinant DNA Technology plasmids, bacteria will then be cultured in a medium.
▪ Target DNA - gene of interest ▪ The transformed bacteria will be able to grow and
▪ Restriction enzymes - used to cut DNA into form colonies on the medium.
fragments.
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▪ The bacteria will divide to produce new identical
bacterial cells.
▪ Each time the bacterial cells divide, the
recombinant plasmids will produce multiple copies
of the target gene.
Summary
• Classical Breeding is anchored to natural mating
while Generic Engineering makes use of a modern
technique to modify the traits of organisms to
achieve better results.
• Biotechnology embraces many branches, from
techniques to improve crops productivity to
manipulation of human genes.
• Recombinant DNA technology refers to various
techniques and procedures used in gene
manipulation
• Polymerase Chain Reaction is a fast and
inexpensive technique used to amplify small
segments of DNA.
LUMEN LEARNING
BIOTECHNOLOGY
- Relying on the study of DNA, genomics analyzes
entire genomes, while biotechnology uses biological
agents for technological advancements.
Key Points
• Genomics includes the study of a complete set of
genes, their nucleotide sequence and organization,
and their interactions within a species and with
other species.
• Through DNA sequencing, genomic information is
used to create maps of the DNA of different
organisms.
• Biotechnology, or the use of biological agents for
technological progression, has applications in
medicine, agriculture, and in industry, which
include processes such as fermentation and the
production of biofuels.
Key Terms
Genomics - the study of the complete genome of
an organism
Sequencing - the procedure of determining the
order of amino acids in the polypeptide chain of a
protein (protein sequencing) or of nucleotides in a
DNA section comprising a gene (gene sequencing).
Biotechnology - the use of living organisms
(especially microorganisms) in industrial,
agricultural, medical, and other technological
applications
• The study of nucleic acids began with the
discovery of DNA, progressed to the study of genes
and small fragments, and has now exploded to the
field of genomics.
• Genomics is 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.
• The advances in genomics have been made
possible by DNA sequencing technology.
• Genomic information is used to create similar
maps of the DNA of different organisms.
• These findings have helped anthropologists to
better understand human migration and have aided
the field of medicine through the mapping of human
genetic diseases.
• Another rapidly-advancing field that utilizes DNA is
biotechnology. This field involves the use of
biological agents for technological advancement.
• The primary applications of this technology are in
medicine (production of vaccines and antibiotics)
and agriculture (genetic modification of crops, such
as to increase yields).
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• Biotechnology also has many industrial
applications, such as fermentation, the treatment of
oil spills, and the production of biofuels.
RECOMBINANT DNA
• Recombinant DNA is the combination of DNA from
two different sources.
• Recombinant DNA technology is useful in gene
cloning and in identifying the function of a gene.
• Recombinant DNA technology can also be used to
produce useful proteins, such as insulin. To treat
diabetes, many people need insulin. Previously,
insulin had been taken from animals.
• Through recombinant DNA technology, bacteria
were created that carry the human gene which
codes for the production of insulin.
• Recombinant DNA technology is used in gene
cloning. A clone is an exact genetic copy. Genes are
cloned for many reasons, including use in medicine
and in agriculture.
Below are the steps used to copy, or clone, a
gene:
1. A gene or piece of DNA is put in a vector, or
carrier molecule, producing a recombinant DNA
molecule.
2. The vector is placed into a host cell, such as a
bacterium.
3. The gene is copied (or cloned) inside of the
bacterium. As the bacterial DNA is copied, so is the
vector DNA. As the bacteria divide, the recombinant
DNA molecules are divided between the new cells.
Over a 12- to 24-hour period, millions of copies of
the cloned DNA are made.
4. The cloned DNA can produce a protein (like
insulin) that can be used in medicine or in research.
Plasmids
• Bacteria have small rings of DNA in the cytoplasm,
called plasmids.
• A plasmid is not part of the bacterial chromosome,
but an additional pieced of DNA.
• When putting foreign DNA into a bacterium, the
plasmids are often used as a vector.
• Viruses can also be used as vectors. The
manipulation of the plasmid DNA, and then the
insertion of the recombinant plasmid into a
bacterium, is an invaluable tool in scientific
research.
• A small round piece of bacterial DNA.
Summary
• Bacteria can produce human proteins.
• Vector DNA is replicated inside a bacterial cell.
• Cloned genes are used in medicine and
agriculture.
• The purpose of antibiotic resistance segments
within a plasmid ensure only bacteria with the
plasmid will grow.
Gene Cloning
• Gene cloning is the process of isolating and
making copies of a gene.
• Gene cloning might be used to isolate and make
copies of a normal gene for gene therapy.
• Gene cloning involves four steps: isolation,
ligation, transformation, and selection.
1. In isolation, an enzyme (called a restriction
enzyme) is used to break DNA at a specific base
sequence. This is done to isolate a gene.
2. During ligation, the enzyme DNA ligase combines
the isolated gene with plasmid DNA from bacteria.
(A plasmid is circular DNA that is not part of a
chromosome and can replicate independently.) The
DNA that results is called recombinant DNA.
3. In transformation, the recombinant DNA is
inserted into a living cell, usually a bacterial cell.
Changing an organism in this way is also called
genetic engineering.
4. Selection involves growing transformed bacteria
to make sure they have the recombinant DNA. This
is a necessary step because transformation is not
always successful. Only bacteria that contain the
recombinant DNA are selected for further use.
Polymerase Chain Reaction
• The polymerase chain reaction (PCR) makes many
copies of a gene or other DNA segment.
• This might be done in order to make large
quantities of a gene for genetic testing.
• PCR involves three steps: denaturing, annealing,
and extension. They are
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repeated many times in a cycle to make large
quantities of the gene.
1. Denaturing involves heating DNA to break the
bonds holding together the two DNA strands. This
yields two single strands of DNA. (Heat to 95C)
2. Annealing involves cooling the single strands of
DNA and mixing them with short DNA segments
called primers. Primers have base sequences that
are complementary to segments of the single DNA
strands. As a result, bonds form between the DNA
strands and primers.
3. Extension occurs when an enzyme (Taq
polymerase or Taq DNA polymerase) adds
nucleotides to the primers. This produces new DNA
molecules, each incorporating one of the original
DNA strands.
Science Behind COVID-19
Virus- obligate intracellular parasite
• Each viral particle, or virion, consists of a single
nucleic acid, RNA or DNA, encoding the viral
genome surrounded by a protein coat, and is
capable of replication only within the living cells of
bacteria, animals or plants. After gaining access to
the specific host tissue, target cell infection is
achieved at the initial stage of virus replication when
the virus recognizes and binds to a receptor on the
target cell surface
Enveloped Virus
SARS-COV-2
▪ Also known as severe acute respiratory syndrome
coronavirus 2, virus that causes coronavirus disease
19 (COVID-19).
▪ highly transmittable and pathogenic viral infection
▪ emerged in Wuhan, China
▪ phylogenetically related to severe acute
respiratory syndrome-like (SARS-like) bat viruses, t
therefore bats could be the possible primary
reservoir.
▪ The intermediate source of origin and transfer to
humans is not known, however, the rapid human to
human transfer has been confirmed widely.
Potential Therapeutic Strategies
▪ Various other anti-virals are currently being
evaluated against infection.
▪ Several other combinations, such as combining
the antiviral or antibiotics with traditional.
▪ Chinese medicines were also evaluated against
SARSCoV-2 induced infection in humans and mice.
▪ Recently in Shanghai, doctors isolated the blood
plasma from clinically recovered patients of COVID-
19 and injected it in the infected patients who
showed positive results with rapid recovery.
Vaccines for SARS-CoV-2
▪ There is no available vaccine against COVID-19,
while previous vaccines or strategies used to
develop a vaccine against SARS-CoV can be
effective. Recombinant protein from the Urbani
(AY278741) strain of SARS-CoV was administered
to mice and hamsters, resulted in the production of
neutralizing antibodies and protection against SARS-
CoV.
Powerpoint Presentation
Week 1
What is Biotechnology?
➢ Technology based on biology
➢ The use of theories and concepts in Biological
Sciences to improve our quality of life.
➢ Biotechnology is simply applied biology. The
areas where Biotechnology is mostly used are in the
fields of:
• Medicine
• Agriculture
• Biofuels
• Genetics
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Genetic Engineering Blunt Ends Vs. Sticky Ends

▪ Also called as Recombination, the products are

called Recombinant DNA

▪ The goal of genetic engineering is to identify traits

that are favorable and insert it in another organism.
In this case, we can have animals or plants with
desirable traits or that they can produce specific
protein.

▪ The most common gene editing tool is CRISPR Name of the enzyme and their recognition and
(clustered regularly interspaced short palindromic cleavage site
repeats)

BT Plant

▪ One good example of a product of Genetic

Engineering is the production of BT Plants.

▪ BT stands for the bacteria Bacillus thuringiensis.

This is a type of bacteria that lives in the soil. These
bacteria are producing proteins that are harmful to
insects specially several species of Moths and
Butterfly.

▪ What happens is that the gene responsible for

producing these proteins are introduced to several
species of plants and become naturally insect.

DNA Cloning Vectors

Target DNA
▪ carry target gene into a host cell, in example,
▪ The gene of interest. Plasmids and Bacteriophage
▪ The cell or organism where the target DNA can be
▪ Plasmid is circular double stranded DNA in a
found is called a donor.
bacteria. It is different from the chromosome.
Restriction Enzymes Though, plasmids carry-out DNA molecules, they
are not capable of manifesting the trait nor produce
the protein.
Host Cell

▪ a bacterial cell that allows the cloning vector to

replicate within it.

▪ The host should be non-pathogenic, harmless

▪ Used to cut DNA into fragments
▪ Restriction enzymes are based from bacteria that
are immune to bacteriophages. They cut specific
segments of the DNA called the restriction sites.
▪ Restriction sites are naturally, 4-8 bases which are
palindromic in nature.
▪ Restriction enzymes may leave sticky ends or
blunt ends.
micro-organism which is easy for cultivation.
Modifying Enzymes
▪ introduces minor bases into DNA or RNA e.g, DNA
Ligase and Taq Polymerase.
▪ Taq polymerase replaces DNA Polymerase in PCR
Cloning
▪ DNA cloning is a molecular biology technique that
makes many identical copies of a piece of DNA,
such as a gene. In a typical cloning experiment, a
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target gene is inserted into a circular piece of DNA
called a plasmid.
▪ There are two types of DNA Cloning:
(A) Molecular Cloning and
(B) Reproductive Cloning.
Dolly the sheep is a byproduct of a Reproductive
Cloning called SCNT or Somatic Cell Nuclear
Transfer.
▪ Most recent were Huahua and Zhong Zhong,
macaques from China
DNA Extraction
▪ Before you start with cloning, you have to extract
first the DNA from a cell.
□ Cells are lysed using a detergent that disrupts the
plasma membrane.
□ Cells contents are treated with protease to destroy
protein and RNase to destroy RNA.
□ Cell debris is pelleted in a centrifuge. The
supernatant (liquid) containing the DNA is
transferred to a clean tube.
□ The DNA is precipitated with ethanol. It forms
viscous strands that can be spooked on a glass rod.
Stage 1: Isolation of a target gene
▪ This process can be done using
(1) cutting the gene from a complete chromosome
using a restriction enzyme or (2) producing a
complementary DNA (cDNA).
▪ To do this the DNA must first be cut into
fragments and the one containing the desired gene
must be identified.
▪ Remember to use the same restriction enzyme
Stage 2: Insertion of a target gene into a vector
▪ Gene is inserted into vectors such as plasmids
and bacteriophages resulting in Recombinant DNA.
Bacterial plasmids that have been isolated from
bacterial cells must be mixed with the same
restriction enzymes used to cut the DNA molecule.
This is done to produce the same sequence of
sticky ends.
Stage 3: Introduction of vector into a host
▪ The plasmids carrying the target gene must be
introduced into a host cell through transformation,
and only a lesser amount will contain the
recombinant plasmid.
Stage 4: Amplification of the target gene by the
host cell (cloning) ad screening
▪ Following the introduction of the recombinant
plasmids, bacteria will then be cultured in a medium.
The transformed bacteria will be able to grow and
form colonies on the medium.
▪ The bacteria will divide to produce new identical
bacterial cells. Each time the bacterial cells divide,
the recombinant plasmids will produce multiple
copies of the target gene.
POLYMERASE CHAIN REACTION
▪ is a method used to amplify DNA, it resembles
replication but is carried out in a test tube.
TOOLS USED IN PCR
1. Thermocycler
2. Test tube containing the DNA sample
3. DNA polymerase (Taq polymerase)
4. primers
5. free DNA nucleotides
THERMAL CYCLER
▪ is a laboratory instrument that heats and cools
samples in repetitive cycles to facilitate DNA or RNA
amplification through the polymerase chain reaction.
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PCR PROCESS
STEP 1: DENATURATION
▪ in which double-stranded DNA templates are
heated to separate the strands;
▪ The reaction temperature is increased to 95 °C,
which melts (disrupts the hydrogen bonds between
complementary bases) all dsDNA into single-
stranded DNA (ssDNA).
STEP 2: ANNEALING
▪ The DNA molecule will be exposed at a lower
temperature to allow the primers to attach to the
Single-Strand DNA. The role of the primer is to let
Taq Polymerase copy the segment.
▪ Taq Polymerase is an enzyme derived from a
bacteria Thermus aquaticus which mimics the job of
DNA Polymerase but can withstand a high
temperature
STAGE 3 – EXTENSION
▪ The temperature will be raised again Taq
Polymerase will copy and texted the segment of
DNA.
▪ after the third step, it is considered that 1 cycle is
complete and there is 22 amount of DNA in the
container (usually an Eppendorf). So after 1 cycle
we can assume that there is 4 copies of DNA.
Evolution
▪ refers to change through time as species become
modified and diverge to produce multiple
descendant species.
▪ it maintains that all diverse forms of life that are
now in existence have come into being through a
gradual and continual process of modification of
ancestral forms.
Selection
▪ process whereby organisms that are better
adapted to their environment survive and reproduce
while those less adapted fail to do so.
▪ it depends upon the existence of phenotypic
variation within the population.
2 Types of Selection
1. Natural Selection
2. Artificial Selection
Natural Selection
▪ is a biological theory that explains why organisms
seem to match their environmental niches so well.
▪ individuals that have certain heritable
characteristics survive and reproduce at a higher
rate than other individuals.
▪ it brings about adaptation and evolution.
Proponent of Natural Selection
Charles Darwin (1809-1182)
▪ Father of Evolutionary thought
▪ Author of the book On the Origin of Species by
means of Natural Selection
▪ One of the organisms he observed to support his
theory was the Beak variation of Galapagos finches.
▪ According to him, Natural selection should be
capable of substantial modification of species over
many hundreds of generations. Even if the
advantages of some heritable traits over others are
slight, the advantageous variations will gradually
accumulate in the population, and less favorable
variations will diminish.
Major Features of Natural Selection
A. Individuals with beneficial traits are more likely to
be 'selected' that is, to have more offspring than
individuals with other, less beneficial traits.
B. When those traits have a heritable component,
they tend to become more common in the next
generation.
C. Alleles with an average result in greater fitness
become more abundant in the next generation, while
alleles with generally reduced fitness become rarer.
D. If the selection forces remain the same for many
generations. beneficial alleles become more and
more abundant, while alleles with lesser fitness
disappear.
Example:
The Galapagos Island has 13 species of finches.
These finches are closely related but differ in the
shape of their beaks. The beak of species is suited
to its food. This suggests that the beak's shapes
evolved by natural selection.
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Types of Natural Selection
1. Stabilizing Selection - genetic diversity
decreases as the population stabilizes on a particular
trait and favors intermediate variants.
Example: Human Birth Weight
2. Disruptive Selection - favors individuals at both
extremes of a characteristic range.
Example: Population of White, Black, and Gray
Rabbits, placed on an environment with black rocks
and white rocks. Both white rabbits and black
rabbits can hide from predators, while gray rabbits
will be eaten.
3. Directional Selection - occurs when a certain
allele has greater fitness than others, resulting in an
increase in the frequency of that allele until it is
fixed in the population gene pool.
Example: Human Height
4. Sexual Selection - special kind of selection that
acts on traits that help animals increase their
chances of mating.
Example: The male peacock has an elaborate train
(tail) to attract the peahen to mate.
5. Polymorphism - many different phenotypes
found in a population, each group represents a
morph (form)
Example: Two morphs of the moth, Boston betularia
Artificial Selection
▪ process of intentional or unintentional modification
of a species through human actions that encourage
the breeding of certain traits over others.
Major Features of Artificial Selection
A. The genotype is altered to produce a new strain
of the organism for a specific purpose.
B. Human preferences or influences have a
significant effect on the evolution of a particular
population or species.
C. Selective breeding, an example of Artificial
Selection, in which particular individuals are selected
for breeding because they possess desired
characteristics or excluded from breeding because
their traits are undesirable.
Examples of organisms that were products of
Artificial Selection
1. Domesticated dogs such as Chihuahua and Great
Dane.
2. Carrots, cabbage, broccoli, cauliflower, brussel
sprouts, collards and kale are al members of
Brassica oleracea.
3. Thorough breed Race-Horsing
4. Cats and dogs originally domesticated for pest
control, hunting or sheepherding were bred to
become working companions.
Negative Effects of Artificial Breeding
1. It removes variation in a population
2. Organisms can be susceptible to diseases or
changes in the environment.
Summary
▪ Evolution modifies all living things and will
continue to produce a change in the future as it is in
the present and past. This module is about Evolution
and how it helped in the diversity of living
organisms. It also tackled the features of Natural
Selection and Artificial Selection.
▪ Evolution is a gradual and continual process of
modification of ancestral forms.
▪ Natural Selection rests on three tenets,
overproduction, variation, and competition.
▪ Artificial Selection involves human actions that
encourage the breeding of certain traits over others.
Evolution
▪ Change in the heritable characteristics of biological
populations over successive generations. These
characteristics are the expressions of genes that are
passed on from parent to offspring during
reproduction.
▪ The central idea of biological evolution is that all
life on Earth shares a common ancestor.
▪ Through the process of descent with modification,
the common ancestor of life on Earth gave rise to
the fantastic diversity that we see documented in
the fossil record and around us today.
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Mechanisms of Evolution Fitness

Terminologies ▪ Describes how successful an organism has been

at passing on its genes.
Population – a group of individuals of the same
species living in a particular area at the same time. ▪ Fitness has a great influence to which trait will be
passed on to the next generation.
Gene Pool – All alleles of a population’s genes
Allele Frequency – The percentage of any one
specific allele Types of Natural Selection

Variations – differences among numbers of a 1. Stabilizing Selection

species ▪ Selection favors intermediate variants.
Genetic Equilibrium – If the allele frequency stays ▪ The intermediate states become more common
the same over many generations. and each extreme variation will become less
common or lost.

Mechanisms of Evolution
▪ Anything that changes the frequency of alleles in a
population is a mechanism of evolution.
1. Natural Selection – Individuals with the best
adapted phenotypes will survive and pass on their
genes to the next generation.
2. Mutation – A mutation in a parents’ DNA could
result in offspring with different alleles, changing the
allele frequency of the population.
2. Disruptive Selection
3. Genetic Drift – Genetic Drift occurs when the
allele frequency of a population changes by chance. ▪ Favors individuals at both extremes of a
characteristics range.
4. Gene Flow (Migration) – Gene flow is any
movement of genes from one population to another.
5. Non-random Mating – If organisms can choose
their mating partners, then the more desirable
alleles will have a higher frequency in future
populations.

Selection
▪ Process whereby organisms that are better
adapted to their environment survive and reproduce
3. Directional Selection
while those less adapted fail to do so.
▪ Occurs when a certain allele has a greater allele
Types of Selection has greater fitness than other resulting in an
1. Natural Selection increase in the frequency of that allele until it is
2. Artificial Selection fixed in the population gene pool.

Natural Selection
▪ is a biological theory that explains why organisms
seem to match their environmental niches so well.
▪ Charles Darwin proposed the theory of natural
selection in his publication, on the origin of species.
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4. Sexual Selection
▪ Special kind of selection that acts on traits that
help animals increase their chances of mating
5. Polymorphism
▪ Many different phenotypes found in a population;
each group represents morph (form).
Artificial Selection
▪ Process of intentional or unintentional modification
of a species through human action that encourage
the breeding of certain trait over others.
Negative Effects of Artificial Breeding
○ It removes variation in a population
○ Organisms can be susceptible to diseases or
changes in the environment.
► Remember, NATURAL SELECTION is not
EVOLUTION. It is a driving force or evolution to
happen.
Genetic Drift
Genetic Drift
▪ is change in allele frequencies in a population from
generation to generation that occurs due to chance
(randomness) events.
Consequences of Genetic Drift
▪ Drift can cause big chances in allele frequency
over time. It may reduce genetic viability in small
populations and may inflict fixation in an allele.
Fixation – refers to the elimination of the allele
▪ Drift is strongest in small populations
▪ Drift is neither predictable in direction in one
generation nor exactly replicable in degree.
Types of Genetic Drift
A. Bottleneck Effect
▪ Happens when the size of a population is severely
reduced. Events like natural disasters (earthquakes,
floods, fires) can decimate a population, killing most
individuals and leaving behind a small, random
assortment of survivors.
Example:
In the Clover City, there are 100 residents. 50 of
them are right-handed and 50 are left-handed. An
unexpected pandemic happened and 75% of the
population died.
• Now in the scenario, we were given a population
that has the same allele frequency for the trait
“handedness”
• The “pandemic” serves as the bottleneck and only
a portion of the population survived.
• This is now the bottleneck effect where there is
now a random chance for an allele frequency to
retain in the population or get fixed.
• The handedness trait has nothing to do with the
survivability o the population so the population
sample will depend on chances of randomness.
B. Founder Effect
• Occurring when a small group in a population
splinters off from the original population and forms
a new one. When a newly formed colony is small, its
founders can
Speciation
▪ The evolutionary process by which populations
evolve to become distinct species.
▪ Formation of new lineages
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Phylogeny
▪ It is the study of relationships among different
groups of organisms and their evolutionary
development.
▪ A phylogenic tree is a diagram that represents
evolutionary relationships among organisms. The
pattern in branching in a phylogenic tree reflects
how species or other groups evolved from a series
of common ancestors.
▪ Cladograms give a hypothetical picture of the
actual evolutionary history of the organisms. It is the
subdivision of living organisms into groups based
on their attributes.
Modes of Speciation
▪ Phylogenetic Tree give an actual representation of
the evolutionary history of the organisms. It is more A. Allopatric Speciation
specifically attempting to reconstruct the order and
▪ Occurs when there is an imbalance of gene flow
possibly the timing of speciation events.
between two population due to physical barrier.

B. Geographic Isolation
▪ Refers to a population of animals, plants, or other
organisms that are separated from exchanging
genetic material with other organisms of the same
species.

How to Read Phylogenetic Trees?

▪ The closer to lines are to each other, the more
closely related the species.
▪ The further away, the more distantly related.

C. Sympatric Speciation

▪ Occurs when there is an overlapping range of the

two diverging species within a region or locality.
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Development of Evolutionary Thought

A number of Scientists and Thinkers have
contributed to the development of the Evolutionary
Thought.
Lamarck’s Theory/Lamarckism

D. Temporal Isolation
▪ When population reproduce at different time

Jean Baptiste Lamarck

▪ The main concept in Lamarckism is the
Inheritance of Acquired Traits.
▪ According to his theory, the bodies of living
organisms were modified through the use and
disuse of certain body parts based on the need of
the organism to adapt to an ever changing
environment.

E. Behavioral Isolation
▪ Population has different rituals or behavior
involved in reproduction.
▪ Above is Lamarck's giraffe (Giraffa camelopardalis)
example.
▪ This theory lack evidence to support the acquired
characteristic today.

Darwin-Wallace Theory
▪ Most believed theory
▪ Natural Selection as a mechanism of evolution
▪ Both Alfred Wallace and Charles Darwin has the
same conclusion
▪ Their ideas can be summaries by the:
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However multiple allelism may cause mutations and
variations
Conclusion 1: There is competition between the
individuals to survive and reproduce. Some
individuals will die young, fail to reproduce or
produce few/ less fit offspring leaving only the fit to
survive to the next generation. • Modern synthesis theory hypothesizes that
speciation is most likely due to the gradual
► Observation 1: In a population,
accumulation of mutations in the gene level.
organisms are capable of producing far more
offspring than is required to replace the
parents.
Evidences of Evolution
► Observation 2: However, the number of
Paleontology/Fossil Records
individuals in the population remains the
same over time except for seasonal ▪ Fossils are body parts of living organisms that are
fluctuations. buried for a long period of time. Fossil records gave
Darwin ideas about the inhabitants of the earth and
Conclusion 2: These differences will determine
their anatomy.
which members will survive and reproduce
successfully, leaving the most offspring. Individuals ▪ Age can be identified by carbon dating.
whose traits best adapt them to their environment
Geographical Distribution
will leave a larger number of offspring. This process
is known as natural selection. ▪ It is believed that the world is consisting of a large
mass of continent called Pangaea.
► Observation 3: Members of a population
differ from one another in their ability to ▪ Because of continental drift, the supercontinent
obtain their needs, withstand extreme splits
environments, and to escape predators.
▪ There are fossil records and species of the same
Conclusion 3: Better adapted individuals will leave origins that can be found in places that were
more offspring. Hence their traits will be passed on believed once connected.
to the subsequent generations. Over many
Example:
generations, the generic composition of the
population will change. This process is called 1. Camels from Asia and North Africa resembles
evolution by natural selection. Llamas of South America
► Observation 4: Much of the variation 2. Darwin's Finches
among individuals is due to genetic
3. Lung Fishes of Africa, South America and
differences and can be inherited,
Australia
4. Marsupials and Monotremes in Australia
Modern Synthesis Theory
Comparative Anatomy
▪ Fusion between Gregor Mendel's Theory of
▪ Similarity in biological structures and function gave
Inheritance and Darwin's Natural Selection
rise to the study of Comparative Anatomy.
▪ Population Genetics as a basis for inheritance
Homologous Structures - same structures different
including genetic variation, natural selection and
function
mendelian inheritance
Modern Synthesis and Darwinism differs in 3 main
points:
• The modern synthesis theory recognizes several
different possible mechanisms of evolution such as
genetic drift, gene flow, mutation pressure versus
Darwinism that only believes in natural selection as
the basis of evolution.
• Modern synthesis theory argues that
characteristics are passed down from parent to
offspring on the parts of DNA called genes.
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Analogous structures - Same Function, Different
Structures
Vestigial Structures - structure of animals that
disappear or deteriorate over a period of time due to
adaptation.
Comparative Embryology
▪ The early development of most vertebrate
embryos are alike. However, in later stages the
similarities are lost
Biochemistry
▪ Studies comparing the biochemistry of different
organisms gives the most persuasive evidence that
all organisms give the most persuasive evidence
that all organisms evolved from a common ancestor.
▪ Comparative biochemistry thus far revealed that:
a. the nucleic acids in almost all organisms have the
same genetic code
b. the metabolic pathways of physiological
processes like respiration is very similar
c. the universal energy used is ATP
Classification System
▪ In order to study the great diversity of organisms
and ecosystems and to effectively communicate
their findings, biologist must organize their
knowledge.
▪ Systematics is the scientific study of the diversity
of organisms and their evolutionary relationships
and an important aspect of systematics is
taxonomy. It is a dynamic science as it involves
constant reevaluation of data, hypotheses, and
theoretical constructs. As new data are discovered
and old data are subjected to reinterpretation, the
ideas change.
Systematics is important as:
A. It can help us understand evolutionary patterns
that can provide information to the origin and spread
of beneficial and harmful varieties
B. It is also useful in predicting characteristics of
newly discovered species
C. New species can be classified based on specific
characters that it shares with other organisms in a
particular grouping so as to record biodiversity
D. Biological knowledge can be communicated
efficiently among scientists
Taxonomy – It is the science of classification and it
involves the naming of organisms (nomenclature).
Classification
▪ Classification is an arrangement of organisms into
groups on the basis of their similarities. The
grouping is done from less inclusive to more
inclusive group until the organisms are assembled
into a final most inclusive group.
▪ The sequence of classification follows a fixed
system of hierarchy of categories such as species-
genus-family-order and so on. The classification
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process includes assigning appropriate position and

rank to a new taxon.
▪ Classification involves arranging organisms into
groups based on their similarities, which reflect
evolutionary relationships among lineages.
Hierarchic Classification
Carolus von Linnaeus created a hierarchical
classification system using seven taxonomic
categories.
1. Kingdom
2. Phylum
3. Class
4. Order
5. Family
▪ As a result, our understanding of how organisms
6. Genus
are related and how we classify organisms are
7. Species continuously changing.

▪ These categories are based on shared physical
characteristics, or phenotypes, within each group.
▪ Beginning with kingdom, each successive level of
classification becomes more and more specific.
▪ Organisms within the same order have more in
common with one another than organisms within
the same class. For example, all species of bears
are mammals, but not all mammals are bears.
▪ There are two types of classification: Artificial
classification system and Natural classification
system.
Artificial System of Classification Vs.
Natural System of Classification
Artificial System of Classification

▪ A useful pneumonic tool to help students
remember the hierarchical classification system is:
“King Phillip Came Over For Green Soup,” with the
first letter of each word representing each category,
beginning with kingdom and ending with species.
○ This classification system is based upon one or a
few easily observable characteristics.
○ It places organisms into groups for purposes of
convenience and economy.
○ Organisms can be placed into groups according to
their color, how they move, habitat or their size.
○ For example, fish can be grouped into freshwater
fish, brackish water fish, and marine fish on the
basis of habitats. Biologists are also able to group
flowers according to color.
Artificial system of classification: Advantage and
Disadvantages Advantages:
Advantages
○ Makes the classification simple and easy
○ Less time consuming and manage to classify with
little information of one or two characters only.
○ Poorly known species can be classified easily.
○ Less instruments of classification are needed.
○ Very specific to the character of choice
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Disadvantages
○ Not universally applicable
○ Cannot initiate bold prediction
○ Since the choice of characters are arbitrary, the
exact correlation cannot be established
○ Various unrelated taxa, which are not at all related
but, similar in one respect only, have been placed
under the same Class.
○ Cannot establish evolutionary relationships among
taxa.
Natural System of Classification
○ This taxonomic system was introduced by Jean
Bauhin in 1623.
○ Generally, this classification is based on many
features, internal as well as external and considers
information from many branches of biology such as
anatomy, biochemical, physiological, morphology,
embryology, and cytology.
Natural system of classification: Advantage and
Disadvantages
Advantages:
○ Makes the classification more inclusive
○ It can be used for bold prediction of ranks and
categories for newly identified species.
○ Contains more exclusive information about the
taxonomic hierarchy.
○ It can help to predict properties of even not-so-
closely related species.
○ Members of different groups are mostly similar in
hereditary pattern.
Disadvantages:
○ The complexity level is more than artificial
○ Combursive and time consuming
○ Less known plants cannot be classified through
this system since their characteristics are not fully
defined.
○ A single property of interest cannot be taken into
consideration for classification
There are two types of natural classification
systems: Phenetic classification system and
Phylogenetic classification system.
Phenetic System of Classification
○ It is based on as many phenotypic similarities
(similarities in appearance) as possible.
○ Hence, the more similarities there are between
two organisms, the more likely these two organisms
belong to the same group. This is a quantitative
approach.
○ In this approach, computer programs are used to
analyze data and group organisms according to the
number of shared characteristics,
(a) Pheneticists believe that it is not important to
differentiate between homology and analogy
(homoplasy) because many more similarities are
due to homology than to analogy.
(b) For example, dolphins and porpoises are
classified as mammals rather than as fish because
they share more similarities with mammals.
○ Thus, the number of similarities that two
organisms have in common reflects the degree of
homology.
○ A dendogram is a family tree based upon this
type of classification
Phylogenetic System of Classification
○ This classification involves grouping organisms
based on shared characteristics which reflect
evolutionary relationships or phylogeny. This
strategy is called evolutionary classification.
○ Biologists now group organisms into categories
that represent lines of evolutionary descent or
phylogeny and not just physical similarities.
○ When biologists compare similarities, they now
consider structural, physiological, development,
behavioural and molecular traits. They look for
homology in different organisms.
○ Cladogram is one of the tools used to classify
organisms in this classification system.
○ A cladogram is used to trace the process of
evolution in a group of organisms based on shared
derived characteristics.
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○ The base of the cladogram represents a common
ancestor for all the taxa.
Each branch point (referred to as a node)
represents the most recent common ancestor. The
node also represents a divergence or splitting of
two or more new groups from a common ancestor.
Dichotomous Key
▪ A tool used to identify and name unfamiliar
organism
▪ Involves characteristics for a specific taxon
▪ Usually, the characteristics are observable
▪ It is composed of statements called leads
▪ The two characteristics must be contrasting
▪ The leads must lead to a new lead up to the
smallest classification
Binomial System of Nomenclature
▪ formal system of naming species of living things
▪ According to this system, each organism is known
my two names – the genus name and the species
name.
▪ These names are all written in Latin.
▪ The name of the genus always begins with a
capital letter.
▪ The species name begins with a small letter.
▪ The scientific names are always italicized.
▪ When handwritten, the genus name and species
name have to be underlined.
A few examples of names of organisms written in
this system:
• Homo sapiens (Human Beings)
• Helianthus annuus (Sunflower Plant)
• Panthera tigris (Tiger)
• Mangifera indica (Mango Plant)
• Canis familiaris (Dog)
Timeline of Classification Systems in Taxonomy
(Zoom in)
Three Domain Classification Scheme
• The three-domain system is a biological
classification introduced by Carl Woose et al. in
1990 that divides cellular life forms into archaea,
bacteria, and eukaryote domains. The key difference
from earlier classifications is the splitting of archaea
from bacteria.
I. Domain Archaea
▪ Classification of living things that lives in harsh
environments (extremophiles)
▪ All are prokaryotes but share some eukaryotic
characteristics in its membrane and chemical
structures.
▪ They resemble bacteria in reproduction and
shapes
Representative Species under Domain Archaea
Methanogens – produces methane
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Thermophiles – lives in extreme hot environment • Are resistant to multiple drugs and are increasingly
like volcanic vents. resistant to most available antibiotics

3. Cyanobacteria

Halophiles – lives in extreme saline environment • Also called as blue-green algae

• A cluster of photosynthetic bacteria

Acidophiles – in extreme acidic environment

II. Domain Eukarya

▪ Classification of living things that are eukaryotic in
nature
▪ Very diverse; has unicellular and multicellular
organisms
▪ Has 4 classifications
Classifications of Eukarya
II. Domain Bacteria
A. Kingdom Protista
▪ Classification of living things that are prokaryotic in
nature. • Unicellular eukaryotes

▪ Formerly classified as Kingdom Monera and • Are either autotrophs or heterotrophs

Eubacteria
▪ Has three shapes: Rod (Bacillus), Round (Cocci),
and Spiral (Spirochaete)
▪ Can be seen alone or in clusters.
Classification of Bacteria
1. Gram-positive bacteria
• Have thicker cell walls
1. Protozoans
• Retains Violet color with crystal violet staining
• Animal-like protists
• Contains peptidoglycan
• Classified according to locomotory organelle

2. Gram-negative bacteria
• Have thinner cell walls
• Does not retain staining
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Examples: 1. Division Basidiomycota

○ Euglena (flagellated) Trypanosoma brucei • Club Fungi
▪ Causes trypanosomiasis or sleeping disease
Examples:
○ Paramecium (cilliated) Paramecium caudatum
○ SHITAKE MUSHROOM (Lentinula edodes)
▪ Found in brackish waters
○ BUTTON MUSHROOMA (Agaricus bisporus)
○ Amoeba (pseudopod) Entamoeba histolityca
▪ Causes amoebiasis in primates 2. Division Zygomycota
○ Sporozoa (no appendage) Plasmodium vivax • Zygote Fungi
▪ Causes malaria
Examples:
○ BLACK-BREAD MOLDS (Rhizopus nigricans)
2. Algae
3. Division Ascomycota
• Plant-like protists
• Sac Fungi
• Classified according to pigment
Examples:
Examples:
○ BREWERS YEAST (Saccharomyces ceraviceae)
○ Chlorophyta (Green Algae) Spyrogyraporticalis
○ CANDIDA (Candida albicans)
○ Phaeophyta (Brown Algae) Sargassum baccularia
4. Division Deuteromycota
○ Rhodophyta (Red Algae) Gracilariacompressa
• Imperfect fungi
Examples:
3. Slime molds
○ PENNICILIN (Penicillium notatum)
• Fungus-like protists
C. Kingdom Plantae
• Classified according to pigment
• Multicellular
Examples:
• All autotrophs
○ Myxogastria (acellular slime molds)
• Has cellulose in cell walls
Physarumpolicephalum
○ Dictyostelid (cellular slime molds)
Dictyosteliumdiscoideum
○ Protestiloid (amoeboid slime molds)
Protosteliummycophaga

B. Kingdom Fungi
• Unicellular and Multicellular
• All heterotrophs and saprophytes 1. Division Bryophyta
• Has chitin in cell walls • Non-vascular plants
• Also called Kingdom Mycota Examples:
○ SILKY FORKLET-MOSS (Dicranella heteromalla)
○ MARCHANTIA (Marchantia polymorpha)
○ ANTHOCEROS (Anthoceros agrestis)
2. Division Tracheophyta
a. Sub-division Angiospermae
• Vascular plants with seeds
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Examples: 3. Phylum Nematoda

○ GUMAMELA (Hibiscus rosasinensis) • Roundworms
○ BANANA (Musa paradisiaca) Examples:
b. Sub-division Gymnospermae ○ Ascaris lumbricoides
• Vascular plants without seeds ○ Ancylostoma duodenale
Examples:
○ LADY FERN (Athyrium filix-femina) 4. Phylum Annelida
○ WHITE PINE TREE (Pinus strobus) • Ringed Worms
○ MAIDENHAIR TREE (Ginko biloba) Examples:
D. Kingdom Animalia ○ Arenicola marina
• Multicellular ○ Lumbricus terrestris
• All heterotrophs ○ Hirudo medicinali
• No cell walls
• There are 36 recognized animal phyla, of which 5. Phylum Arthropoda
but nine contain the vast majority of described,
• Segmented body, and paired jointed appendages
extant species.
Examples:
○ Mantis religiosa
○ Parasteatoda tepidariorum
○ Carcinus maena

6. Phylum Echinodermata
• Spiny Skins
Examples:
○ Asterias rubens
○ Echinus esculentus
○ Pentacta pygmaea
1. Phylum Porifera
• Sponges
7. Phylum Cnidaria
Examples:
• Hydra and Medussa
○ Geodiabarretti
Examples:
○ Halichondria bowerbanki.
○ Hydra oligactis
○ Aureliaaurita
2. Phylum Platyhelminthes
• Flatworms
6. Phylum Chordata
Examples:
• Vertebates
○ Dugesia japonica
Examples:
○ Fasciola hepatica
○ CLASS AGNATHA - Petromyzon marinus
○ Taenia solium
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○ CLASS CHONDRICHTYES - Carcharodon

carcharias
○ CLASS OSTECHTYES – Chanoschanos
○ CLASS AMPHIBIA – Limnonectes magnus
○ CLASS REPTILIA – Crocodylus mindorensis
○ CLASS AVES – Pithecofaga jefferyi
○ CLASS MAMMALIA – Homo sapiens