GENETIC ENGINEERING
direct manipulation of genes for practical with stress-related conditions
purposes. The applications of genetic engineering
include the manufacture of hundreds of useful
products.
-with the use of biochemical and mechanical tools
of DNA technology, scientists can make
recombinant DNA in vitro.
-they can introduce the DNA into cultured cells
that replicate the DNA and may express its
genes.
The modification of traits may involve:
I. introduction of new traits into an organism
II. enhancement of a present bait by increasing
the expression of the desired gene.
III. enhancement of a present bait by disrupting
the inhibition of the desired gene's expression
MODIFYING TECHNIQUE:
CLASSICAL BREEDING - focus on the mating of
organisms with desirable qualities.
Examples: controlled pollination of plants
mating of animals with desired traits.
RECOMBINANT DNA TECHNOLOGY
molecular biology techniques are being employed
in the insertion and expression of proteins in
different organisms for various purposes.
GENERAL OUTLINE OF RECOMBINANT DNA
1. cutting or cleavage of DNA restriction enzymes
2. selection of an appropriate vector or vehicle
which would propagate the recombinant DNA
3. ligation (join together) of the gene of interest
(eg from an animal) with the vector but bacterial
plasmid
4. transfer of the recombinant plasmid into a host
cell (that would carry out replication to make huge
copies of the recombined plasmid
5. selection process to screen which cells actually
contain the gene of interest
6. sequencing of the gene to find out the primary
structure of the protein
PLASMIDS
a small circular double-stranded DNA
molecule found in bacteria and some other
microscopic. organisms
-they carry only few genes and exist independent
of chromosomes, the primary structures that
contains DNA in cells
-Able to self-replicate and can be picked up from
the environment and transferred between bacteria
-They are used by their host organism to cope
BIOLISTICS
It is a 'gene gun' technique 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
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 is said to make the cells atly
"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 30 min
-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
minute then back to 4°C for 2 minutes
-the rapid rise and drop of temperature increase
and decrease the pore size 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 method is commonly used for
insertion of genes into mammalian cells
-this technique follows a similar methodology as
Heat shock Treatment, but, the expansion of the
membrane pores is done through an electric
"shock"
CENTRAL DOGMA OF MOLECULAR BIOLOGY
states that genetic information flows only
in one direction, from DNA, to RNA, to protein, or
RNA directly to protein
DNA (gene)
RNA (transcript)
PROTEINS (trait)
Based on the central dogma, if transcription and
translation of genes lead to some traits, then the
insertion of certain genes in may provide it with
new traits a given organism
PCR AMPLIFICATION
(Polymerase Chain Reaction)
a technique that allows the detection of specific
genes in target organisms.
A laboratory technique for rapidly
producing (amplifying) millions to billions of
copies of a specific segment of DNA.
DNA AMPLIFICATION
The production of multiple (millions to billions)
copies of a sequence of DNA
→ PCR is used to amplify a specific region a DNA
strand (the DNA target)
-most PCR methods typically amplify DNA
fragments of up to 10 kilo base pairs (kb),
although some techniques allow for amplification
of of fragments up to 40 kb in size
Earth
-The Earth is 4.6 billion years old
-Life on Earth arose around 3.5 billion years ago
-Humans did not exist with dinosaurs as what
movies usually depict
-man could have first appeared about 100-150
thousand years ago as shown by artefactual
evidence in various sites.
GEOLOGIC TIME SCALE
The geologic time scale divides up the history the
earth based on life-forms that have existed during
specific times since the creation of the planet.
Their divisions are called geochronologic units.
The Geologic Time Record is a tabular
representation of the major divisions of the
Earth's history.
-Most of these life-forms fossils, which are found
the remains or traces of an organism from the
geologic past that has been preserved in
sediment or rock. SP
The Geologic Time scale is divided by the
following divisions:
EONS: longest subdivision; based on the
abundance of certain fossils.
ERAS: Next longest subdivision; marked by major
changes in the fossil record.
PERIODS: Based on types of life existing at the
time
EROCHS: Shortest subdivision; marked by
differences in life forms and can vary from
continent to continent.
Geologist over time have put the time scale
together piece by piece
-units were named as they were discovered -
sometimes unit names were borrowed from
geography, from a person, or from the type of
rock that dominated the unit.
THE GEOLOGIC TIME SCALE
CAMBRIAN - from Latin name for Wales. Named
for exposure of strata found in a type-section in
Wales by British geologist Adam Sedgwick.
DEVONIAN - named after significant outcrops
first discover near Devonshire, England.
JURASSIC - named for representative strata first
seen in the Jura mountains by German geologist
Humboldt in 1795
CRETACEOUS - from the Latin "creta" meaning
chalk by a Belgian geologist.
FOUR LARGE SEGMENTS OF EONS
HADEAN- the earliest time of the Earth
-period of time for which we have no rock record.
ARCHEAN- corresponds to the ages of the oldest
known rocks on Earth.
PROTEROZOIC - called the Precambrian Eon.
PHANEROZOIC - the remainder of geologic time,
including the present day.
Cambrian Explosion - is the belief that there was
a sudden, apparent explosion of diversity in life
forms about 545 million years ago.
-created most of the major extant animal groups
today
-the start of the Cambrian was characterized by
the breaking up of supercontinent Gondwana.
Early scientist who contributed to shaping and
developing evolutionary thought.
Charles Darwin
Alfred Russel Wallace
Carolous Linnaeus - considered as the "Father of
taxonomy". Most Famous for creating a system of
naming plants and animals we still use today.
Thomas Malthus - English Economist and
demographic best known for his and theory that
population growth will always tend to outrun the
food supply and that betterment of humankind is
impossible without strict limits on reproduction.
Georges Cuvier - called the founder of
Comparative anatomy and it was his knowledge
in his field that accounted for his well-known and
abstract uncanny ability, reconstruct animals from
only fragments of fossil remains.
D. James Hutton - discovered evidence that earth
and its features are shaped by very slow and
gradual processes history over extremely long
spars of time. This proves as Uniformitarianism.
E. Charles Lyell - a Scottish geologist geological
discoveries informed a revelatory of in our
understanding of the Earth and its history.
B. Jean Baptiste Lamark's theory on evolution of
change
A. Principle of use and disuse - Suggested that
body parts used more frequently become stronger
and those not used deteriorate.
B. Inheritance of acquired characteristics -
Proposed that traits acquired during an organisms
lifetime offspring can be passed on the organism.
FOSSILS
- A fossil is the preserved remains of an organism
that has died
- Fossils tell scientists, called paleontologists,
about living things such as their biology and
environmental conditions over Earth's history
through the rock record. In addition, they give
clues to the conditions of the earth (i.e.. climate)
at the time that the fossil was preserved and
possibly relate changes of an organism over time.
index fossils
(guide fossils/indicator fossils / one fossils)
Fossils from short-lived organisms that lived in
many places, used to define and identify geologic
periods.
-trilobite
-echinoid
-graptolite
-coral
-brachiopods
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types of fossils
MOLDS- Impression made in a substrate
negative image of an organism.
EX: shells
CASTS - when a mold is filled in
EX: Bones and Teeth
PETRIFIED - Organic materialis converted into
stone.
EX: Petrified Trees, coal balls
ORIGINAL - Preserved wholly (frozen in ice, trap
in jar pits)
EX: Woolly mammoth Amber from the Baltic
region.
REMAINS - dried dessicated inside caves etc.
CARBON FILM- Carbon Impression on
sedimentary rock.
EX: leaf impression
TRACE / Ichnofossils- Record the movements
and behaviors of the organism.
EX: Trackways, tooth. marks, gizzard mits etc.
UNALTERED PRESERVATION
Small organism or part trapped in amber,
hardened plant sap.
PERMINERALIZATION / PETRIFICATION
the organic contents of bones and wood are
replaced with silica, calcite or pyrite, forming a
rock-like fossil.
REPLACEMENT
hard parts are (replaced) dissolved and replaced
by other minerals, like calcite, silica, pyrite moth,
or iron.
CARBONIZATION OR COALIFICATION
the other elements are removed and only the
carbon remained.
RECRYSTALIZATION
hard parts are converted to more stable minerals
or small crystals turn into larger crystals
AUTHIGENIC PRESERVATION
molds and casts are formed after most of the
organism have been destroyed or dissolved.
DATING FOSSILS
used to determine a precise age of a fossil by
comparing into it to similar rocks and fossils of
known ages.
RELATIVE DATING
I. Based upon the study of layer of rocks
II. Does not tell the exact age: only compare
fossils older or younger, depends on their position
in rock layer.
III. Fossils in the uppermost rock layer / strata are
younger while those in the lowermost deposition
an oldest.
RULES OF RELATIVE DATING
A. Law of Superposition.
Sedimentary layers are deposited in a specific
time-youngest rocks on top, oldest rocks at the
bottom
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 I fault is YOUNGER
than the rock it cuts through.
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 radio) decay products of radioactive
isotopes are stable atoms mining mass of C-14
overtime.
A living organism has carbon-14. For the amount
of Carbon in the organism's body to become half,
it will take about 5,700 years, which is half-life of
C-14.
Importance of fossil record to human evolution
Overall, the fossil record serves as a critical than
source of reconstructing the story of human
evolution and understanding our place in the on
Earth broader context of life.
SPECIES
•Emst Mayer's definition; "Species are group of
inter the breeding natural populations that are
reproductively isolated from other such groups. "
•The biological concept states that a species is a
species group of populations whose members
have the potential to interbreed in nature and
produce viable fertile offspring: they do not breed
successfully from other populations.
REPRODUCTIVE ISOLATION
The existence of biological factors (barriers) that
impede two species from producing viable, fertile.
• It is the property that inhibits two species from
mating
We can divide these forces into two separate
categories pre-zygotic forms and past zygotic
forms.
REPRODUCTIVE ISOLATING MECHANISM
Reproductive isolation can be classified by
whether factors act before or after fertilization.
The species maybe separated before mating in
PRE-ZYGOTIC isolation or may occur after
fertilization in POST-ZYGOTIC isolation
Zygote is a fertilized egg all that results from a
union of female gamete (egg, or ovum) with male
gamete (sperm).
Hybrids are offspring of crosses between different
pecies.
Pre-zygotic isolation -isolution mechanisms
prevent fertilization and zygote with formation.
pre zygote barriers block fertilization from
occurring by:
-impeding different species from attempting to
mate preventing the successful completion of
mating
-hindering fertilization if mating is successful
GEOGRAPHIC/ECOLOGICAL/HABITAT
ISOLATION - refers to the place where the
organisms mate potential mate occupies different
areas of habitat thus, they never come in contact.
two species encounter each other rarely, or not at
all, because they owupy different habitats, even
though not isolated by physical barriers.
B.TEMPORAL OR SEASONAL ISOLATION
different groups may not be reproductively mature
at the same season, or month or year.
species that breed at different times of the day.
different seasons, or different years cannot mix
their gametes.
C. BEHAVIORAL ISOLATION
patterns of courtship are different
• courtship rituals and other behaviors unique
species are effective barriers.
D. MECHANICAL ISOLATION
• morphological differences mating. Can prevent
successful
• differences in reproduction organs prevent
successful interbreeding.
E. GAMETIC ISOLATION
• incompatibilities between egg and sperm
prevent fertilization
• sperm of one species may not be able to fertilize
eggs to species.
POST-ZYGOTIC ISOLATION
• isolation mechanism allow fertilization but
nonviable or weak, or sterile hybrids are formed
•post zygotic barriers prevent the hybrid zygote
from developing into a viable, fertile adult.
HYBRID IN VIABILITY
• fertilized egg fails to develop the early embryo
stages
• genes of the different parent species may
interact and impair the hybrid's development
HYBRID STERILITY
hybrids are sterile because gonads develop
abnormally or there is abnormal segregation of
chromosomes during meiosis
HYBRID BREAKDOWN
51 hybrids are normal, vigorous and viable, but 2
contains many weak. First-generation hybrids
sterile individuals are fertile, but when they mate
with another species or with either parent
species, offspring of the next generation are
feeble of sterile.
SPECIATION
ALLOPATRIC SPECIATION
Geographic speciation Callo- other, patric place;
`other place')
-Occurs when some members of a population
become geographically separated from the other
members thereby preventing gene flow
• the two populations become genetically different
• Examples of geographic barriers are bodies of
water and mountain ranges
Regions with many geographic barriers typically
have more species than do regions with fewer
barriers.
Reproductive Isolation between populations.
generally is increases as the distance between
them increases
SYMPATRIC SPECIATION
Sympatric speciation (sym -same, patric - place,
'same place')
Occurs without geographic isolation
• speciation takes place within a single
population.
example is change in chromosome number
(polyploidization)
POLYPLOIDY
Polyploidy is the presence of extra sets of
chromosomes due to accidents during cell
division.
much more common in plants than in animals An
autopolyploid is an individual with more than two
chromosome sets, derived from species. one
many important crops (oats, cotton, potatoes,
tobacco. and wheat) are polyploids.
SEXUAL SELECTION
• Sexual Selection can drive sympatric speciation
•for mates of different colóns distributed to
speciation
PARAPATRIC SPECIATION
Parapatric speciation (para- beside, patric-place;
beside each other)
Occurs when the groups that evolved to be
separate spesies are geographic neighbors.
Gene flow occurs but with great distance is
reduced.
There is also abrupt change in the environment
over a geographic border selection and strong
disruptive innovation must also happen.
GENETIC MECHANISMS
Genetic mechanisms that change and change
genotype the Frequencies of populations
MUTATION
change in the DNA sequence of an organism due
to errors in DNA replication during cell division
exposure to mutagens or a viral infection,
exposure to mutagenic agents like radiation or
certain chemicals
• it is the primary source of genetic variation upon
which natural selection acts and the only way
which new variation enters the species
GERMLINE MUTATIONS
occurs in gametes
these are especially significant because they can
be transmitted to offspring and every cell in
offspring will have the mutation.
SOMATIC MUTATIONS
occurs in other cells of the body have little effect
on the organism because they are confined to just
one cell and its daughter cells cannot be passed
to offspring
How it happens?
Mutations results from either of the two course (1)
error in DNA replication during cell division or
(2) exposure to cell damaging mutagens such as
chemicals and radiation, which causes the
structure of individual nucleotides to change.
Types of Mutations
Chromosomal Alteration - change the
chromosome structure. Occurs when a section of
a chromosome breaks off and rejoins incorrectly
or does not rejoin. very serious and causes major
changes in the genetic material.
Point mutation - a change in a single nucleotide in
DNA usually less serious than a chromosomal
alteration changes happen in the genetic code of
an organism.
Frameshift mutation - deletion or insertion of one
or more nucleotides that change the reading
frame the base sequence. Mutations can occur in
both animals or plants
SELECTION - process by which certain traits or
alleles become more or less common in a popula
over time due to their effect on reproductive
success
preferential survival and reproduction or preferent
elimination of individuals with certain genotypes
employing natural or artificial controlling factors.
The theory of evolution by selection was
proposed by Charles Darwin and Alfred Russel
Wallace in 1858.
Natural Selection, a key mechanism of evolution
proposed by Charles Darwin, favors traits that
increase an organism's chances of survival and
reproduction in a given environment.
TYPES OF SELECTION
Natural Selection - the basic mechanism of
evolution the process which is also known as
"Survival of the fittest"
nature or the environment dictates which among
the organism will survive, the organisms has d
certain variety of traits or characteristics that will
be passed on the next generation.
Artificial Selection or Selective Breeding when
humans selectively choose organisms with
specific characteristics as breeding stock, they
are performing the role of environment.
- the breeder attempts to isolate those genotypes
that are responsible for plant or animal's desired
qualities in a sustainable environment.
- the qualities are economically or aesthetically
desirable to humans, rather than useful to the
organism in its natural environment
GENE FLOW/MIGRATION
-from one population to a different population -
movement of genes between populations same
species
-this movement occurs through the migration of
individuals who interbreed with members of other
populations, leading to the exchange of genetic
material
-can take place between two populations of the
same species and is meditated by reproduction
and vertical gene transfer from parent to
offspring.
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helps to maintain genetic diversity within a
species and can counteract the effects of genetic
drift.
EXAMPLE
A bee carrying pollen from one flower population
to another.
GENETIC DRIFT
-also called genetic sampling error or seawall
wright effect
-the random fluctuation of allele frequencies in a
population due to chance events.
-occurs in all population but is particularly
significant in small populations where chance
events can have a greater impact.
-can lead to the loss of genetic variation and the
fixation population of certain alleles in a
population.
Living Things
here are some biomolecules which may be used
to prove relationships. These chemicals include
DNA and proteins. The building ding blocks of
these chemicals may be analyzed to show
similarities and differences among organisms.
The more similarities, the closer the relationships.
Cytochrome-c
-protein and important enzyme found in all
organisms.
-highly conserved protein which functions in the
electron transport chain system of the
mitochondria needed for the release of energy
which is from food.
-alle performs a role in apoptosis (programmed
cell death) by being released into the cytosol
activating the events of cell
-*the molecules are assumed to have descended
from a existed over primitive microbial
cytochrome that two billion years ago.
CLADOGRAM
-it is also called branching tree that can be to
show the relationship among the organisms.
-the data can then be tabulated to show the
number of differences.
-basic features (cells and anatomical structures
also be used to infer relationship among
organisms
-this types of cells (prokaryotic or eukaryotic)
presence and numbers of limbs, and presence of
wings or hair can be compared to show
relationships which can be plotted cladogram.
-Vertebrates possess common structures
(pharyngeal gill clits, notochord, dorsal nerve
cord, and post-anal tail) which are present in the
embryo stage and are lost, modified, or become
vestigial in adult forms.
-the presence of these structures implies descent
from common ancestor
-A complex cladogram can then be created to
how the positions of the organisms in the
evolutionary tree
Evidence of evolution
Evidence from fossils
Evidence from structures
Evidence from Embryology
Evidence from Molecular Biology
Evidence from Biogeography
EVIDENCE FROM FOSSILS
are remains in of ancient organisms trapped in
rocks, tar pits, frozen in ice, or embedded in
amber
-records found in the rock shows a gradual
evolutionary descent in from simpler to be more
gradual complex life forms.
-Paleontologists use the fossils found in rocks to
track the evolutionary history of many organisms.
EVIDENCE FROM STRUCTURES
sructures in different organisms can be compared
inter common in lineage
Homologous structures
Analogous structures
Vestigial Structures
HOMOLOGOUS STRUCTURES
same set of bones that presumably from a
common ancestor.
-they appear different and may have varied
functions
ANALOGOUS STRUCTURES
- perform the same function, different structure
- have very different embryological development
VESTIGIAL STRUCTURES
have lost most of their ancestral function
has lost its original function through the course of
evolution
EVIDENCE FROM EMBRYOLOGY
Embryology is the study of the development of an
organism from an embryo to its adult form.
Common structures are shared in the embryo
stage and disappear by the time the embryo
reaches the juvenile or adult form.
EVIDENCE FROM MOLECULAL BIOLOGY
Many organisms have similar molecules of life
(DNA, RNA, proteins) that suggests descent from
a common ancestor with modifications.
EVIDENCE FROM BIOGEOGRAPHY
geography is the study of geographical
distribution of fossils and living organisms.
Organisms usually arise in areas where similar
organisms already exist.
Similar organisms may also be found in different
locations which could mean that the two places
were probably connected.
closely related species are usually found in areas
at are geographically close to each other.
SYSTEMATICS BASED ON EVOLUTIONARY
RELATIONSHIPS:
Tree of life and Systematics
Taxonomy
cladistics and Phylogeny
SYSTEMATICS
is the study of kinds and diversity of organisms
and all relationship.
Tracing phylogeny evolutionary history of a
species is one of the goals of systematics.
-use data ranging from fossils to molecules genes
to infer evolutionary relationships
- these information enable biologists to construct
meth comprehensive tree of life
Lines of evidence to infer evolutionary
relationships
+ Fossill evidence
+ Homologies
+ Biogeography
+ molecular clock
Molecular closk is a technique used in
evolutionary biology to estimate the timing of
divergence events between species of
populations.
BIOLOGISTS use phylogenetic trees for:
- testing hypotheses about evolution
-learning about the characteristics of extinct
species and ancestral lineages.
-classifying organisms
Taxonomy
Classification has become an essential part of
everyday life, and the habit can be useful.
Classification
method of grouping organisms
arranging entities in order for cataloguing and
expressing relationships between these entities
Hierarchy
system of organizing groups into ranks according
to status, level, importance or power.
Nomenclature
Formal naming of taxa according to some
standarized system
•International code of Botanical Nomenclature
- International code of Zological Nomenclature
Identification
the process of associating an unknown taxon with
a known name
Description
- the assignment of features or attributes to a
taxon
Taxonomy
- the theory of and practice of classifying
organisms.
- major part of systematics
LINNAEAN SYSTEM OF CLASSIFFICATION
•LINNAEAN TAXONOMY - All the real knowledge
have depends on the method by which we
distinguish the similar or dissimilar.
Binomial system of Nomenclature introduced by
Linnaeus.
 Bi - two
 Nomial/nomen - name
generic name and specific ephitet genus
generic name and specific name
•genus – capital
•epithet – low
• Species – bold italic
•Carolus Linnaeus (1707-1778)
- devise the taxonomic system
- is a hierarchical system since organism are
grouped into ever more inclusive categories from
species to kingdom.
• Carl Woere (1981)
propose a category higher than kingdom called
domain.
Cladistics and Phylogeny
-studies relationships between taxa using shared
derived characters
-members of ancestor and a group share thus a
common recent more "closely related" to one
another than to other group of organisms.
CLADE
- a group of taxa consisting of an ancestor and all
of its descendant taxa
- share a set of derived characters.
FAMILY TREE
-show how people are related to each other -used
to show relationships between individuals.
can also be used to see ancestral connections.
GENETIC PEDIGREE
- a visual representation of several generations
-show how family members are related