BIOLOGY 5.

Expression  Introducing allergins and toxins to foods

Genetic engineering: - Coded for by the donor DNA.  accidental cross pollination
- addition, manipulation, and deletion - multiple genes  antibiotic resistance
- IT ALLOWS GENES FROM ONE ORGANISM TO
BE INSERTED INTO A CELL OF A DIFFERENT 6. Transformation PROS in GM foods
ORGANISM OF A DIFFERENT SPECIES. – the process by which organisms take up and  increased pest and disease resistance
express foreign DNA  grow food in harsh climate
Deoxyribonucleic Acid (DNA)  increased food supply
-the material in a cell that stores and encodes genetic  more nutritional value
Gene cloning
information IT IS ESTIMATED THAT THE EARTH FORMED
– using bacterial transformation to make lots of copies of a
desired gene. ALONG WITH THE SOLAR SYSTEM 4.6 BILLION
double helix YEARS AGO (4,600 MYA)
– composed of structural units called nucleotide
GENETIC ENGINEERING APPLICATIONS: GEOLOGIC TIME SCALE A SUMMARY OF THE
1. Agriculture MAJOR EVENTS IN EARTH’S HISTORY
Chromosomes
-Productive, less fertilizer, Disease Resistant 1. EON – largest segment of geologic time
- structures found in the center (nucleus) of cells that carry
long pieces of DNA 2. ERA
2. Medicine 3. PERIOD
Genes - Genetic diseases become prevalent. 4. EPOCH – smallest segment of geologic time
- basic unit of heredity • serve as the blueprints for proteins - vaccines: form protective anti bodies
- hormones: bacterial cells can be factors to produce human Finding age of rocks using RELATIVE TIME
Genetic Code
insulin 1. Law of superposition
- genetic code is universal
– all living things have A, T, C and G in their DNA - oldest in the bottom, youngest in the bottom
gene therapy
Gene Expression -modify human DNA to repair or to replace faulty gene, 2. Law of cross cutting relationship
- is the process by which the instructions in our DNA are cystic fibrosis the best known disease. - igneous intrusion is younger.
converted into a functional product, such as a protein. gene pharming- First mammal engineered is Tracy the
Sheep (1990) 3. Law of included fragments
Plasmid
- small circular double stranded DNA - fragments found in another rock layer is older than the
Genetically Modified Organism (GMO) rock layer is came from
- naturally exists in bacterial cell and also to some
- insert DNA from one organism to another to achieve
eukaryotes
desired Trait. 4. Faulted and Folded layers
1. Isolation
Biotechnology - these rocks must have been present before the actions of
- Isolation of plasmid from a bacterial cell
- The material application of biological science to create faulting and folding took place.
2. Cutting
products derived from organisms.
- Restriction Enzymes = molecular scissors and cut DNA in
specific sites called Restriction sites Outcrop
Transgenic Organism
- organisms that contains DNA from another species. - exposed rock layers at the earth’s surface

3. Ligation
Transgenes Key Bed
- Rejoining cut fragments of DNA and forming artificial
- Genes that have moved between organisms. - thin wides spread layer (volcanic ash) that can be
recombinant molecules.
correlated an exact point of time.
COMMON GM FOODS
4. Transformation
- soybeans, corn, cotton
- recombinant DNA introduces into bacteria cell. Fossil
CONS in GM foods
- any evidence of earlier life preserved in the rock.
 RADIOCARBON DATING
Original Remains (rare) - use radioactive isotope carbon 14 found in all living
things. Can be used to date back about 100 000 years.
- the actual unchanged remains of the plants or animal are
preserved. Precambrian
- 88% of earth’s history
Replaced Remains
- soft part of the original animals have dissapeared and the
hard pats have been by mineral material (petrified wood)
Mold
- fossil shell and bone are dissolved complete out of the Paleozoic- (ancient life)
rock leaving a hollow depression on the rock. The end of the Paleozoic era is called the “Age
of Amphibians.”
Casts – Early land plants including mosses, ferns and
- new mineral fills the mold. cone-bearing plants.
– The early coal forming forests were also
Trace Fossils formed during this time.
- impressions left in the rock (footprints, trails rocks – Much of the limestone quarried for building and
borrow) industrial purposes, as well as the coal deposits of
western Europe and the eastern United States,
Finding age of rocks using ABSOLUTE TIME were formed during the Paleozoic.
1. Tree rings – The Cambrian (beginning) opened with the
- each ring represents single year (spring/fall) the width of breakup of the world-continent Rodinia and
the ring depends upon the temperature and rainfall. closed with the formation of Pangaea, as the
2. Varves Earth's continents came together once again. This
- Glacial Lake deposits, A thick light-colored layer in the event is thought to have caused the climate
changes that led to mass extinction event.
summer and a thin dark layer in the winter.
-- At the end of the Paleozoic, the largest mass
RADIOACTIVE DATING
- use to date far back in time, certain rock contains extinction in history wiped out approximately
radioactive isotopes. 90% of all marine animal species and 70% of
land animals
radioactive isotopes
- are atoms of elements that give off radiation from their – Possible causes of this Mass Extinction Event
nuclei. • Lowering of sea levels when the continents were
rejoined as Pangaea (convergent boundary)
Radioactive Decay • Increased volcanic activity (ash and dust)
- is a process where radioactive isotope changes into new
stable element.
• Climate changes – cooler climate
-- early Fish don’t have jaws
-- Marine animals that resemble clams
MEZOSOIC ERA (middle life)
•At the beginning of this era the continents were
joined as Pangaea.
•Pangaea broke up around the middle of this era.
•Reptiles became the most abundant animals
because of their ability to adapt to the drier
climate of the Mesozoic Era.
– Skin maintains body fluids
– Embryos live in shell
• Dinosaurs were also very active in this era.
– First small dinosaurs appeared in the Triassic
Period.
– Larger and more abundant dinosaurs appeared
in the Jurassic Period.
• Small mammals and birds also appeared during
this era.
– The mammals were small, warm-blooded
animals. Hair covering their bodies.
• Gymnosperms or plants that produce seeds, but
no flowers (Pine Trees)
• Flowering plants appeared during the END of
this era
• This era ended with a mass extinction event
about 65 million years ago.
– Many groups of animals, including the
dinosaurs disappeared suddenly at this time.
• Many scientists believe that this event was
caused by a comet or asteroid colliding with
the Earth.
CENOZOIC ERA (recent life )
• Began about 65 million years ago
– Climate was warm and mild.
– Marine animals such as whales and FOSSIL 3. VESTIGIAL STRUCTURES
- the preserved remains or traces of an organism that is no – reduced body parts (in comparison to the same
dolphins evolved. longer living. complex structure in other organisms) that have little to
• Mammals began to increase and evolve -Usually found in sedimentary rocks. no function, remnant of an ancestor
Examples:
adaptations that allowed them to live in Types of Fossils:
• Human appendix (other mammals
many different environments 1. IMPRINT
it is necessary to aid in digestion)
– thin, soft object (leaf, feather) is buried and sediments
– land, air, and the sea. later harden
• Human external ear muscle
(useless, but still there)
– Grasses increased and provided a food 2. MOLD
• Human tailbone (coccyx)
– Buried organism disappears and leaves an empty space.
source for grazing animals 3. CAST
• Human wisdom teeth
• Bird wings – Penguins adapted for
• Many mountain ranges formed during the – mold filled by minerals (replica of organism)
swimming, ostrich wings for
Cenozoic Era 4. PETRIFICATION
balance and courtship
-minerals replace hard parts (bones, teeth, etc.) of organism
– Alps in Europe and Himalayas in India; 5. AMBER
Biochemical Similarities
•Similarity of proteins, RNA & DNA molecules
Rocky Mountains in the USA – entire organism fossilized in tree sap
•The more closely related organisms are, the more similar is
6.FROZEN
• Growth of these mountains may have – entire organism frozen in ice
the biochemical makeup
•Indicates common ancestor
helped to cool down the climate (Ice Ages 7. TRACE
•Universality of genetic code – supports evolution
occurred late in the Cenozoic Era – footprints, trails, etc.
•Similar chemistry & structure of chromosomes among
(Quaternary Period). Law of Superposition
Eukaryotes
•Chlorophyll is the same basic molecule in all
• As the climate changed, the animals had - The most basic principle of dating rocks and the remains
photosynthetic organisms
of organisms inside is “the deeper it is, the older it is.”
to adapt to the rise and fall of the oceans What can fossils show?
caused by melting glaciers. • Organisms have appeared and disappeared, and have
Common Ancestor
changed over time
• This era is sometimes called the “Age of - the most recents species from which two different species
• Extinction of species
have involved.
Mammals” • Transitional forms reveal links between groups:
Archaeopteryx: between reptiles & birds’
- flowering plants Comparative Anatomy
Eustheopteron: amphibious fish
- study of anatomical structures to find similarities and
- marine and land animals difference.
Seymouria: reptile-like amphibian
-Study of anatomical structures to find similarities and
differences
Embryology
EVIDENCE OF EVOLUTION 1. HOMOLOGOUS STRUCTURES
-Patterns of embryological development can indicate a
• EVOLUTION – parts with similar basic structure (derived from same
common ancestry
- genetic change in a population of organisms over time structures in embryo—same common descent) but may
-All vertebrate embryos exhibit pharyngeal pouches at a
vary in function.
certain stage of their development. These features, which
4 Types of Evidence that scientists have gathered in support 2. ANALOGOUS STRUCTURES
develop into neck and face parts, suggest relatedness.
of evolution: – structures that have the same function (may look
1. Fossils somewhat alike), but have different structures and DO
Recombinant DNA technology
2. Comparative Anatomy & Structures NOT have a common descent
-Allows DNA to be combined from different sources
3. Embryology •Example: wings have developed independently in insects,
-Also called genetic engineering or transgenic
4. Biochemistry (Proteins & DNA reptiles, birds, and bats
Vector
– DNA source which can replicate and is used to carry
foreign genes or DNA fragments.
Recombinant DNA
– A vector that has taken up a foreign piece of DNA
Restriction enzyme
– an enzyme which binds to DNA at a specific base
sequence and then cuts the DNA. It is named after the
bacteria from which they were isolated.
Recognition site
– specific base sequence on DNA where a restriction
enzyme binds
A restriction map
- is a diagram of DNA showing the cut sites of a series of
restriction enzymes
Steps of Bacterial Transformation
1. Choose a bacterial host
a. E. coli is a model organism
i. Well studied, No nuclear membranes,Has enzymes
necessary for replication, Grows rapidly (20 min. generation
time), Inexpensive ,Normally not pathogenic, Easy to work
with and transform
Characteristics of a useful plasmid
i. Single recognition site
- Plasmid only cuts in one place,
ii. Origin of replication
- Allows plasmid to replicate and make copies for new cells.
iii. Marker genes
- Identifies cells that have been transformed.
iv. gene for antibiotic resistance
– bacteria is plated on media with an antibiotic, and only
bacteria that have taken up a plasmid will grow
v. gene that expresses color
– bacteria taken up a recombinant plasmid are a different
color than bacteria that have taken up a NON recombinant
vector
2. Prepare bacterial cells for transformation.
a. Treat with calcium chloride
– softens the phospholipid bilayer of the cell membrane,
which allows the plasmid to pass through
b. Electroporation
– brief electric pulse
c. Directly inject plasmid into bacterial host
3. Plate transformation on appropriate media
a. Contains nutrients for bacteria and antibiotic to
distinguish transformed bacteria from Non transformed
bacteria
4. Incubate plates overnight
a. E.coli grows at body temp. (37 °C) 6. Analyze plates.
How do you identify and clone a gene of interest?
DNA library
– a collection of cloned DNA fragments from a particular
organism , Can be saved for a relatively long period of time
and screened to pick out different genes of interest
Two types of libraries
1. Genomic library
– contains DNA sequences from entire genome
2. cDNA library
– contains DNA copies of mRNA molecules expressed
DNA Technology
- technology involved in genetic engineering that can be
used to cure diseases, to treat genetic disorders, and to
improve food crops
HUMAN GENOME PROJECT
- Initiated in 1990 with plan to identify all human genes
- Francis Collins, and Craig Venter
- consider ethical,legal, social issues
Model Organisms
1. E. Coli
2. Arabidopsis Thallana
3. Saccharomcyes cerevisiae
4. Drosophila Melangaster
5. Caenorhabditis Elegans
6. Mus musculus
Polymerase chain reaction (PCR)
- A lab technique used to amplify segments of DNA
"PCR has transformed molecular biology through vastly
extending the capacity to identify, manipulate and
reproduce DNA.
Reaction requirements for PCR
1.Template DNA
– total genomic DNA isolated from an organism that
contains a target region to be amplified
2.DNA primers
- short pieces of single stranded DNA that flank the target
3.Taq DNA polymerase
- Attaches nucleotides on the growing strand of DNA
4.Nucleotides (GATC)
– Polymerase adds complementary nucleotides to the
template Reactions are placed in a machine called a
thermal cycler.
DNA FINGERPRINTS:
1. The banding patterns of DNA fragments from two
different individuals may be compared to see if they are
related (ex. Paternity tests)
2. DNA fingerprints of members of two different species
can be compared to determine how closely species are
related.
3. Using DNA fingerprints to compare samples of blood,
hair, or tissue found at a crime scene with a suspect’s
blood sample may help in solving crimes.
Human Growth Hormone
- used as a treatment for dwarfism; causes bones to
elongate.
Interferon
- used to treat viral infections and cancer by preventing the
replication of viruses
Interleukins
- used to treat HIV and cancer by activating and stimulating – is any group of species designated by name.
different kinds of white blood cells
Sister taxa The following rules apply to reconstructing a phylogeny:
Reproductive Cloning - are groups or organisms that share an immediate common 1. Maximum likelihood
-Involves the making of a whole new organism from a ancestor. - states that when considering multiple
still living organism. phylogenetic hypotheses,
-There is no sexual reproduction or fertilization involved True clade 2. Maximum parsimony
- is a monophyletic group that contains a common ancestor - states that says when considering multiple
Macroevolution: Phylogenies and all of its descendants. explanations for an observation.
Taxonomy
- is the classification of organisms based on shared paraphyletic group
characteristics. - is one that has a common ancestor but does not contain all
 originated with Carolus Linnaeus in the 18th century. of the descendants.
Order of taxonomy from largest to smallest:
1. DOMAIN polyphyletic group
2. KINGDOM - does not have a unique common ancestor for all the
3. PHYLUM descendants.
4. CLASS
5. ORDER Anagenesis
6. FAMILY - is the accumulation of changes in one species that leads to
7. GENES speciation over time.
8. SPECIES -It is the evolution of a whole population.
Domains- A Recent Development Cladogenesis
 Carl Woese proposed three domains based the rRNA - is the budding of one or more new species from a species
differences prokaryotes and eukaryotes. The that continues to exists.
prokaryotes were divided into two groups Archaea and • During the course of evolution, traits change. The
Bacteria. original shared trait is termed the ancestral trait and the trait
 A taxonomic unit at any level of hierarchy is called a found in the newly evolved organism being examined is
taxon. termed the derived trait.
 Classifying organisms according to their shared • Any feature shared by two or more species that is
characteristics is also indicative of their evolutionary inherited from a common ancestor is said to be homologous.
history. -The limbs above are homologous structures, having similar
 Phylogeny bones.
- the study of the evolutionary relationships among a
group of organisms. Why Analogous Structures Exist
 A phylogenetic tree Analogous structures
–is a construct that represents a branching “treelike” - evolve as a result of similar selection pressures. These two
structure which illustrates the evolutionary animals are both burrowing mammals yet are not closely
relationships of a group of organisms. related.
Phylogenies are based on:
 Morphology and the fossil record The molecular clock
 Embryology - hypothesis states: Among closely related species, a given
 DNA, RNA, and protein similarities gene usually evolves at reasonably constant rate.
-These mutation events can be used to predict times of
taxon evolutionary divergence.