REVIEWER FOR LONG QUIZ 1

CENTRAL DOGMA OF
MOLECULAR BIOLOGY - is a
theory stating that genetic
information flows only in one
direction, from DNA to RNA, to
protein, or RNA directly to protein
- also explains the flow of genetic
information, from DNA to RNA, to
make functional product, a protein

 It suggests that DNA contains

the information needed to
make all of our proteins, and
that RNA is a messenger that
carries the information to the
ribosomes
 The ribosomes serves as
factories in the cell where the
information is ‘translated’
from a code into the functional
product

GENE EXPRESSION - the process  DNA replication- is the

by which the DNA instructions are biological process by which a
converted into the functional product cell makes an exact copy of its
- has two stages transcription and DNA, which is essential for cell
translation division and inheritance of
genetic information
 In transcription, the information - It occurs in the nucleus of the
in the DNA of every cell is Eukaryotic cells and cytoplasm of
converted into small, portable the Prokaryotic cells and involves
RNA messages the separation of the DNA double
 During translation, these helix, followed by the synthesis of
messages travel from where the complementary strands using
DNA is in the cell nucleus to the existing DNA as a template
ribosomes where they are ‘read’ - This process ensures that each
to make specific proteins daughter cell receives an identical
 The central dogma states that set of genetic information to the
the pattern of information that parent cell during cell division.
occurs most frequently in our - DNA strands separate and serve
cells is: as templates for the production of
1. From existing DNA to make new new DNA molecules.
DNA(DNA replication)
2. From DNA to make RNA FEATURES OF REPLICATION
(transcription) 1. Semi conservative - the resulting
3. From RNA to make new proteins DNA consists of one old and one
(translation) new strand
2. Complimentary - Base pairing is  DNA Polymerase III - main
maintained; Adenine pairs with enzyme for synthesizing the new
Thymine, Guanine pairs with DNA strand in a 5’ to 3’ direction
Cytosine, new DNA molecules are  DNA Polymerase I - removes
produced in the 5’ to 3’ direction RNA primers and replaces them
3. Semidiscontinuous - the leading with DNA; has a proofreading
strand is synthesized in a continuous function
manner (5’ to 3’) while the lagging  Ligase - seals nicks or gaps in
strand is produced discontinuously in the DNA by forming
short stretches called Okazaki phosphodiester bonds
fragments  Exonuclease - removes
incorrect nucleotides from the
 In lagging strand synthesis, newly synthesized DNA strand;
there is a need for a primer proofreading activty
terminus which is provided by an  DNA Polymerase II and IV -
RNA molecule. RNA is involved in DNA repair, can fix
synthesized by a primase or damaged DNA during replication
RNA polymerase. The 3’OH of or in response to environmental
the RNA is where new DNA factors
nucleotides are added thus new  DNA Ligase I - seals nicks in
DNA is built in the 5’ to 3’ the DNA during the final stages
direction. of replication and DNA repair
Enzymes in replication are as  Endonuclease - removes
follows: damaged or mismatched DNA
1. Helicase segments during DNA repair
2. Gyrase
3. SSB (single strand binding
proteins)
4. Primase or RNA polymerase
5. DNA polymerase
6. DNA ligase

ENZYMES INVOLVED IN THE

PROCESS OF DNA REPLICATION
 Helicase - unwinds the double-
stranded DNA, creating a
replication fork
 Topoisomerase - relieves
tension ahead of the replication
fork by making and resealing
temporary cuts in DNA
 Single-Strand Blinding
Proteins - binds to single-
stranded DNA to prevent re-
annealing and stabilize the
strands
 Primase - synthesizes RNA
primers complementary to the
template DNA strand
STEPS INVOLVED IN THE polymerization in the 3’ to 5’
PROCESS OF DNA REPLICATION direction.
1. Initiation - begins at the origins of  As it approaches the terminator
replication with helicase unwinding sequence, it terminates and
the DNA releases the newly synthesized
2. DNA Unwinding - single-strand RNA strand. The newly released
binding proteins keep the DNA RNA strand further undergoes
strands apart post-transcriptional modification
3. Primer Synthesis - primase  DNA is unwound and one strand
creates RNA primers as starting is used as template for the
points production of an RNA molecule
4. DNA Synthesis - DNA  An RNA polymerase makes
polymerases add nuceotides to form RNA in the 5’ to 3’ direction
new strands  Specific regions in the DNA
5. Leading and Lagging Strands - called promoters allow the
DNA polymerases add nucleotides binding of transcription factors
to form new strands which make possible the binding
6. Okazaki Fragment Processing - of RNA polymerase
the leading strand is made  Three major types of RNA are;
continuously; the lagging strand in messenger RNA(mRNA),
Okazaki fragments transfer RNA (tRNA), and
7. Termination - RNA primers are ribosomal RNA (rRNA)
replaced with DNA, and fragments
are joined by DNA ligase
8. Proofreading and Repair - DNA
polymerases correct errors, and
repair mechanisms fix the damage
9. End Result - two identical DNA
molecules with one old and one new
strand

TRANSCRIPTION OR RNA
SYNTEHSIS

TRANSCRIPTION - is the process

by which the information is
transferred from one strand of the
DNA to RNA by the enzyme RNA
Polymerase
- the DNA strand which undergoes
this process consists of three parts
namely promoter, structural gene
and a terminator
- the DNA strand that synthesizes
the RNA is called the template
strand and the other strand is called
the coding strand. The DNA- REVERSE TRANSCRIPTION - is
dependent RNA polymerase binds to the transfer of information from RNA
the promoter and catalyzes the to make DNA, this occurs in the case
of retroviruses, such as HIV. It is the
process by which the genetic
information from RNA is assembled
into DNA

TRANSLATION OR PROTEIN
SYNTHESIS
 This occurs in the ribosome.
Basic ingredients are the various
types of RNAs produced in
transcription and some proteins
or enzymes. The mRNA
contains triplets of bases called
codons that specify an amino
acid, eg. UUU-phe
 Various tRNAs carry amino
acids from the cytoplasm to the
actual site of translation in the
ribosome
 A tRNA has an anticodon that
pair with a codon in the mRNA.
Different rRNAs combine with
ribosomal proteins to make up
the sub-units of a ribosome. A
functional ribosome has a small
and a large sub-unit.
 In bacteria, transcription and
translation may be simultaneous
 In eukaryotic cells, mRNA, tRNA,
and rRNA travel from the
nucleus to the cytoplasm
through the nuclear pores. RNAs
may undergo processing
 Some unnecessary parts like
introns are removed. In
eukaryotic mRNA, a 5’ cap and a
3’poly A tail are added. Coding
regions of mRNA are called
exons. They specify functional
protein products
REVIEWER FOR QUIZ IN GENERAL
BIOLOGY 2

GENETIC ENGINEERING - involves

the use of molecular techniques to
modify the traits of a target organism
- the modification of traits may involve
the introduction of new traits into an
organism as to enhancement of
present traits by increasing the
expression of the desired gene or 2. SELECTION - the most commonly
by disrupting the inhibition of the used as vectors are plasmids (circular
desired genes’ expression DNA molecules that originated from
 It includes classical breeding bacteria, viruses and yeast cells).
which is considered the traditional Plasmids are not part of the main
way of genetic engineering which cellular genome, but they carry genes
practices the mating of organisms that provide the host cell with useful
with desirable qualities and properties such as drug resistance,
mating ability and toxins production.
RECOMBINANT DNA They ae small enough to be
TECHNOLOGY- a modern technique conviniently manipulated
of genetic engineering experimentally and furthermore, they
 It is the joining together of DNA will carry extra DNA that is spliced to
molecules from two different them
species. The recombined DNA 3. LIGATION - (eg. from animal) with
molecule is inserted into a host the vector (cut bacterial plasmid) as
organism to produce new genetic shown on step 3 of the above diagram.
combinations that are of value to The resulting molecule is called
science, medicine, agriculture, and recombinant DNA. It is recombinant in
industry the sense that it is composed of DNA
from two different sources.
GENERAL OUTLINE OF 4. TRANSFER OF THE
RECOMBINANT DNA follows: RECOMBINANT PLASMID INTO A
1. Cutting - by restriction enzymes HOST CELL - (that would carry out
(REs) as shown on steps 2 on the replication to make huge copies of the
diagram. Restriction enzymes are recombined plasmid). In the above
called “molecular scissors” cutting diagram as shown in steps 4, the host
the DNA at specific target sequences cell is a bacterium known also as
leaving a single-stranded overhang at recombinant bacterium which will
the site of the cleavage (step 2). undergo cloning or replication of
These overhangs of the donor DNA recombinant DNA
(gene of interest) will be paired with 5. SELECTION PROCESS TO
other overhangs (vector DNA) SCREEN WHICH CELLS ACTUALLY
CONTAIN THE GENE OF INTEREST
- The next step after cloning, therefore,
is to find and
isolate that clone among other
members of the library. If the library
encompasses the whole genome of an
organism, then somewhere within that
library will be the desired clone.
6. SEQUNCING OF THE GENE TO
FIND OUT THE PRIMARY
STRUCTURE OF THE PROTEIN -
Once a segment of DNA has been
cloned, its nucleotide
sequence can be determined. The 1. BIOLISTIC - a “gene gun” is used
nucleotide sequence is the most to fire DNA-coated pellets on plant
fundamental level of knowledge of a tissues. Cells that survive the
gene or genome. It is the blueprint that ‘bombardment’, and are able to take
contains the instructions for building up the expression plasmid coated
an organism, pellets and acquire the ability to
and no understanding of genetic express the designed protein.
function or evolution could be 2. PLASMID INSERTION BY HEAT
complete without obtaining this SHOCK TREATMENT - Heat Shock
information. 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 (usually with CaCl2) is
said to make the cells “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 30min. 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 1
minute then back to 4°C for 2 minutes.
The rapid rise and drop of temperature
is believed to increase and decrease
the pore sizes 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” .
 - an inhibitor (I.e antisense RNA)
disrupts the expression of this gene,
thereby delaying the softening of the
fruit and extending the time it may be
kept in storage and transported to
markets

3. ELECTROPORATION - . This BT-corn(Bacillus thuringiensis)

technique follows a similar corn - was developed to
methodology as Heat Shock incorporate the production of a toxin
Treatment, but, the expansion of the (I.e Bt-endotoxin) from Bacillus
membrane pores is done through an
thuringiensis in corn plants
electric “shock”.This method is
 This toxin results in the death of
commonly used for insertion of genes
into mammalian cells. pests that feed on these plants
like the corn borer larvae
GENETICALLY MODIFED  The toxin has been shown to be
ORGANISM - it is a plant, animal, selective for Lepidoptera larvae
microorganism or other organism and is non-toxic to humans,
whose genetic makeup has been mammals, fish and birds
modified in laboratory using genetic
engineering or transgenic technology BT eggplant - the selective toxicity
 This creates combinations of plant, of the toxin allows its use in
animal, bacterial and virus gens foodcrops. The introduction of the
that do not occur in nature or toxin is believed to increase crop
through traditional crossbreeding production due to decreased losses
methods from pest infestation. The same
 With the ability to insert gene
technology has been applied in the
sequences, comes the possibility
Philippines for the development of
of providing new traits for these
target organisms. This has allowed Bt-eggplant
the development of GMOs
 Some of these genetic ETHICAL ISSUES
modifications promise higher  Despite the proposed benefits of
produc yield for their targets. GMOs, some people have raised
These include the Flavr-Savr their concerns regarding the
Tomato and Bt-Corn consumption of these modified
foods
Flavr-Savr Tomato - was the first  While most of the products are
genetically modified organism that was tested for safety, concerns are
licensed for human consumption. This raised for the possibility of not
trait modified in this tomato is its being able to detect hazards that
ripening process. are present, but are currently
- a gene for an enzyme that causes undetectable by today’s current
the degradation of pectin in the cell technology.
walls (I.e polygalacturonase) normally  Because of these issues,
softens the fruit as it ripens manufacturers are urged to provide
 labels that notify consumers of that the consumers must be
GMO presence in their products. provided with enough information
 While GMOs are believed to be to make their own choices
safe when licensed by the food regarding their use.
regulatory agencies, it is believed

LESSON 3: EVOLUTION AND

ORIGIN OF BIODIVERSITY

KEY POINTS
 The Earth’s history is divided into
eons, eras, periods and epochs
 The geologic time scale is a
record of the life forms and IT SIMPLY BE SUBDIVIDED THIS
geological events in Earth’s history WAY:
 Scientists developed the time scale 1. PRE-CAMBRIAN LIFE (HADEAN,
by developing by studying the rock ARCHAEN AND PROTEROZOIC
layers and fossils worldwide ERAS) - it covers approximately 88%
 Radioactive dating was used to of the Earth’s history. During this time
determine the absolute divisions in that the Earth was transformed from a
the time scale ball of gas and dust to liquid rock
enveloped with hot, non-breathable
DIVISIONS gases mostly composed of carbon
EONS - longest subdivision, based on dioxide, nitrogen and sulfur
the abundance of certain fossils - the molten rock cooled down to form
ERAS - next to longest subdivision, the Earth’s crust and with that, the
marked by major changes in the fossil gases also changed providing a cooler
record temperature composed mostly of
PERIODS - based on types of life nitrogen
existing at the time - the Earth become more conductive
EPOCHS- shortest subdivision; to life and allowed single-celled
marked by differences in life forms and cyanobacteria to exist
can vary from
continent to continent.
 3. MESOZOIC ERA - it started 245
million years ago and lasted for 180
million years
- subdivided into three periods:
Triassic, Jurassic, and Cretaceous
periods
- these are the major geological
2. PALEOZOIC ERA - this era known events that happened during this
as “Old Life”, started more than 540 era;movement of the tectonic plates
million of years ago and lasted for like the gradual rifting of the
more than 300 million years. supercontinent
- this era id divided into six periods: Pangaea. This split Pangaea into two
Cambrian, Ordovician, Silurian, northern continent (North America and
Devonian, Crboniferous, and Eurasia) and Laurasia and a southern
Permian continent, Gondwana (South America,
Australia, Antarctica and the Indian
continent).
4. CENOZOIC ERA - this era started
65 million years
ago and continues up to the
present time. It is divided into three
periods: Paleogene,
Neogene and Quaternary.
- the world’s great mountain ranges
were built during this era. The main
Alpine orogeny, which produced the
Alps and
Carpathians in southern Europe and
the Atlas Mountains in northwestern
Africa, began roughly between 37 to
24 million years ago.
FOSSILS - are the preserved remains
of plants and animals whose bodies
were buried in sediments, such as
sand and mud, under ancient seas,
lakes and rivers.
- also include any preserved trace of
life that is typically more than 10 000
years old.

LESSON 4: BASIC MECHANISMS

OF EVOLUTION
’
LESSON 5: EVOLUTION AND
ORIGIN OF BIODIVERSITY:
PATTERNS OF DESCENT WITH
MODIFICATION
LESSON 6: DEVELOPMENT OF
EVOLUTIONARY THOUGHT