Module 4 : The Central Dogma of Molecular Biology also makes DNA a relatively stable

molecule as it is less likely to get

Central Dogma of Molecular Biology involved in chemical reactions.
- Basic underlying principle in the field of genetics.
- Explains that DNA codes for RNA, which codes
for proteins.

The nitrogenous bases in the nucleotide can be

classified according to the number of rings in their
structure.

1. Purines - which are adenine and guanine have

a double-ringed structure.
Components of the Central Dogma of Molecular
Biology
2. Pyrimidines - which are cytosine, thymine and
uracil contain only one ring in their structure.
❖ Deoxyribonucleic acid (DNA)
- The genetic material passed on from
parents to offspring.
- Contains the instructions necessary for
the survival of every organism.
- In prokaryotes such as bacteria, DNA is
located in the nucleoid region in the
cytoplasm.
- In eukaryotes, DNA is located in the
membrane-bound nucleus, but some
may be found in the mitochondria.
- Biologists Francis Crick and James
Watson in 1953 proposed a DNA model The nitrogenous bases undergo complementary base
that is a double helix structure that pairing wherein each pai should contain a purine and a
twists spirally, similar to a twisted ladder pyrimidine. Each nucleotide is paired together by forming
or a spiral staircase. hydrogen bonds.

In DNA, adenine is paired with thymine and guanine is

paired with cytosine. Uracil replaces thymine in RNA.

DNA molecules are very long. In fact, an Escherichia

coli bacterium found inside the large intestine of humans
may contain DNA that has close to five million base
pairs. Surprisingly, E. coli can measure only at least 1.6
micrometers but the length of its DNA molecule is
roughly 1.6 millimeters. This means that the DNA
molecules are folded into a space in only 0.001 of its
length.

❖ Ribonucleic acid (RNA)

- A single-stranded molecule that is also
composed of nucleotides with a few
modifications.
- The sugar backbone of RNA is ribose.
- The backbone or building block of the
- At the cellular level, your DNA serves as
DNA is called the nucleotide is
the “manual”, and the RNA serves as its
composed of a phosphate group, a
“photocopy”.
sugar and nitrogenous bases.
- If the cell needs an information that
- Deoxyribose is the sugar group in
codes for a specific protein, RNA will
DNA. Deoxy in “deoxyribose” means
copy that information stored in the DNA.
that ribose has lost an oxygen atom.
(sa ganitong way, nacocopy ng RNA
- The absence of an oxygen atom on the
ang information sa DNA pero intact pa
second carbon in the deoxyribose sugar
den yung information sa DNA; protected
helps distinguish DNA from RNA which
ang info)

➔ Different types of RNA


1. Messenger RNA (mRNA)
- Translates the genetic code into
proteins with the help of
ribosomes.
- Located in the nucleus and
cytoplasm
(yung structure ng mRNA, para siyang ladder or hagdan)
2. Transfer RNA (tRNA)
- Helps in transferring amino
acids to the correct sequence in
the mRNA
- Located in the cytoplasm
(structure naman ng tRNA, para siyang cross)
3. Ribosomal RNA (rRNA)
- Structural component of
ribosomes
- Located in the ribosomes
People originally thought that RNA only helps in creating
proteins. However, it was recently discovered by
biologists that RNA also can act as enzymes that helps
speed up chemical reactions in the body. It also helps in
regulating various cell processes, ranging from cell
division, differentiation and growth to cell aging and
death. Certain RNA defects can also result in human
diseases.
❖ Proteins
- Final products in the central dogma of
molecular biology.
- Called the building blocks of life
because they have diverse functions in
the body.
- Composed of polymers of numerous
amino acids known as polypeptides.
- The three-dimensional structure of a
protein not only defines its size and
shape, but also its function. The folding
in a protein structure allows for
interactions between amino acids that
are distant to each other.
➔ Functions of Proteins
- Serves as structural support.
Collagen is a good example of this as it
supports youtube body and connects
your muscles and bones together.
Collagen also makes up your hair and
skin.
- Proteins aid in transporting
molecules around your body.
Hemoglobin (found in red blood cells) is
the prime example of this as it carries
oxygen from your lungs to all parts of
the body.
- Proteins also acts as enzymes. Your
salivary glands, stomach and intestines
create different kind of enzymes that
break down the food you eat into
nutrients that can be absorbed by your
cells.
- Acts as a passageway of molecules
and substance into and out of the cell.
Scientists have identified 20 amino acids so far. These
amino acids can potentially be configured into more
unique information-carrying structures. The properties
of the proteins are determined by the order of the
amino acids in the polypeptide.
Genetic code is the language of instruction in the
mRNA. It uses a combination of only three letters at a
time. Thus, each word of the coded message is three
bases long. The three-letter combination in the mRNA is
known as a codon.
Three codons are referred to as STOP codons- UAG,
UGA and UAA.
Replication, Transcription, and Translation

❖ DNA Replication
- Ensures that each cell has the complete
set of DNA molecules during cell
division.
- During this, DNA molecules separate
into two complementary strands which
both of these strands can serve as a
template for a new strand.
- Enzymes unzip DNA molecules by
breaking down the hydrogen bonds
between base pairs.
➔ Three major steps:
1. Initiation
- First major step in DNA
replication.
- In this process, an enzyme
called helicase unwinds and
separates the DNA into two
single strands.
- The starting point or the origin of
replication happens in adenine
and thymine because only two
hydrogen bonds are in between
them.
- On the other hand, guanine and
cytosine have three hydrogen
bonds in them.
- The structure formed from this
process is called the replication
fork.
- RNA primase binds the RNA
nucleotides to the initiation point
of the 3’-5’ parent strand.
- RNA nucleotides act as the
primer or the starting point for
DNA synthesis.
- Once the primer nucleotides are
attached to the template DNA,
the RNA primase exits in
preparation for elongation.
2. Elongation
- Occurs when an enzyme called
DNA polymerase adds DNA
nucleotides to the 3’ ends of the
newly synthesized strand.
- Because of the different
arrangement of the carbon
atoms in the two strands, the
elongation process has two
different versions. Both versions
occur simultaneously.
- One version is called the
leading strand wherein it
involves the continuous
replication of nucleotides to the
5’-3’ template strand by the
DNA polymerase.
- The other strand is the lagging
strand wherein it involves the
discontinous replication in the
3’-5’ template strand,
- Okazaki fragments are the
different chunks of DNA
(nangyayari to kasi yung lagging
strand hindi siya continously
nababasa ng DNA polymerase
so ang nangyayari, numerous
RNA primers bind at various
points along the lagging strand)
- Later on, these Okazaki
fragments are joined together.
3. Termination
- The last step in DNA replication.
- In this process, the DNA
polymerase halts when it
reaches a section of the DNA
template that has already been
replicated.
- However, this event does not
end the entire DNA replication
process.
- In the lagging strand, there are
gaps where the primers were
present. These primers have
been removed because an
enzyme called exonuclease
strips the RNA primers away.
These RNA primers need to be
replaced with DNA.
- An enzyme called ligase seals
up the sequence into two
continuous double strands,
resulting in two DNA molecules.
- The DNA replication process is
usually described as
semiconservative because half
of the DNA is composed of the
old template strand and the
other half is composed of the
newly synthesized strand.
In DNA replication, all processes should be controlled.
The “proofreading” function of the DNA polymerase
helps prevent mistakes in the replication process.
❖ Transcription
- Process by which mRNA is synthesized
from DNA.
- First stage in the central dogma of
molecular biology.
- Happens when a DNA portion is copied
to form its complementary mRNA
sequence.
- For prokaryotes, transcription occurs in
the cytoplasm.
- In eukaryotes, it occurs in the nucleus.
➔ Three Steps of Transcription
1. Initiation
- Requires an enzyme known as
RNA polymerase which is
similar to DNA polymerase.
- RNA polymerase uses only one
strand of DNA as a template to
create a strand of mRNA.
- RNA polymerase binds at
specific sequences in the DNA
nucleotides called the
 promoters, which serve as
initiation sites for the enzyme.
2. Elongation
- Only one of the unmounted DNA
strands acts as a template for mRNA
synthesis.
- Happens when different nucleotides
from the cytoplasm are added to the
growing RNA chain.
- Similar to DNA replication, RNA is also
synthesized in the 5’-3’ direction.
3. Termination
- Happens when RNA polymerase
reaches the terminator site.
- The terminator site contains a specific
sequence of nucleotides that signals the
end of transcription.
- When this happens, transcription stops
along with the release of the RNA
polymerase and the transcribed mRNA
strand.
- The terminator consists of a series of
adjacent adenines, which is preceded
by a nucleotide palindrome that stops
the RNA polymerase from transcribing
any further.
- Then, the DNA double helix forms.
❖ Translation
- Sequence of nucleotide bases created
in mRNA after transcription serves as a
code for the order of amino acids to be
joined together.
- Happens when the message carried by
mRNA is decoded into a protein or a
polypeptide chain.
➔ Three Steps in Translation
1. Initiation
- Where the mRNA transcribed inside the
nucleus is released into the cytoplasm.
- It starts when the ribosomal subunits,
especially the small subunit binds to the
5’strand of the mRNA until it encounters
the start codon (AUG)
- The presence of the codon initiates
translation.
- Anticodon is composed of a set of three
nitrogenous bases in the tRNA molecule
that is complementary to one of the
mRNA codons.
- Allows the cell to use instructions from
mRNA to create proteins.
2. Elongation
- As each of the codon moves through
ribosomes, the proper amino acid is
brought into the ribosome and is
attached to the growing polypeptide
chain.
- It is simply the growing polypeptide
chain by bringing in the proper tRNA to
translate the mRNA into a protein.
3. Termination
- Continuous attachment of tRNA to the
mRNA allows the polypeptide chain to
elongate until it encounters a STOP
codon (UAA, UAG, UGA) which
terminates and completes the process
of translation.
- There are no tRNA molecules with
anticodons for STOP codons.
- The stop codon would signify protein
release factors that would release the
polypeptide from the ribosome.
- Then, the ribosomes splits into its
subunits, which can be later
reassembled for another round of
protein synthesis.
In summary, gene expression happens when DNA is
transcribed into a molecule of mRNA, which is then
translated into a defined sequence of amino acids in a
protein.
Module 6 : History of Life on Earth
The history of life on earth tells you the origin of all life-
forms.
- First widely accepted area of how life on Earth
formed was proposed by the Russian chemist
Alexander Ivanovich Oparin (1894-1980).
- Oparin proposed that the atmosphere of early
Earth was a very reactive atmosphere, with
numerous incidents of lightning and high levels
of ultraviolet radiation. Because of this highly
reactive atmosphere, Oparin thought that the
early oceans contained a solution of many
essential elements and compounds. He referred
to it as “primordial soup” wherein the earliest
forms of life arose through a series of reactions
that made simple compounds become complex.
- History has its remnants.
The Origin of Life
- Earth was not formed from a single event.
- The earth was formed by different pieces of
cosmic debris that were probably attracted to
one another over a course of about 100 million
years.
- As it was forming, it was struck by one or more
meteor like objects, possibly one as large as
Mars.
- The collision most probably produced enough
heat to melt the entire globe and when Earth
melted, the different elements contained in it
rearranged themselves according to density.
- The densest elements formed the core of Earth.
- From there, radioactive decay generated
enough heat to convert the interior of Earth into
molten rock while those who are considered
moderate dense elements, which include
hydrogen and nitrogen, formed the atmosphere.
- The infant planet is so different from the modern
earth because the sky was most probably
pinkish orange, and its early atmosphere
contained hydrogen cyanide, carbon dioxide,
carbon monoxide, nitrogen, hydrogen sulfide
and water. As you can imagine, no life forms can
ever survive that harsh environment.
First Organic Molecules

- Earth in its early form had very harsh conditions.
- American chemists Stanley Miller and Harold
Urey conducted an experiment in the 1950s
to find out if organic molecules could evolve
from inorganic molecules accompanied with the
harsh conditions of early Earth.
- They conducted an experiment which involved
simulating the early conditions of Earth inside
the laboratory.
- In their experiment, they filled a flask with
hydrogen, methane, ammonia and water to
represent the early atmosphere of Earth and
made sure that no microorganisms would
contaminate it.
- Then, they passed electric sparks through the
mixture to simulate lightning. After a few days,
they noticed that amino acids (building blocks of
proteins) began to accumulate in their setup.
Which was surprising because amino acids are
not single compounds at all.
- Even though scientists now know that Miller and
Urey’s original simulation of the earthly
atmosphere is inaccurate, their experiment was
still significant as it suggested that organic
compounds necessary for life might have arisen
from simple inorganic materials present on
primitive Earth.
- Importantly, this experiment has not only
encouraged many other experiments to find out
the origin of life; it also helped in contributing
knowledge to science.
How Life Began
- Scientists believe that microscopic cell-like
structures similar to modern bacteria appeared
200-300 million years after Earth cooled enough
to carry water.
- These large organic molecules are known as
proteinoid microspheres which have a
selectively permeable membrane that allows
certain molecules to pass through them like
cells.
- Proteinoid microspheres also had a simple
means of storing and releasing energy in and
out of their systems.
- Several hypotheses suggest that structures
similar to proteinoid microspheres might have
acquired more cellular characteristics.
Evolution of RNA and DNA
- One of the hypotheses about the origin of life
suggests that RNA could have evolved before
DNA due to three conditions.
1. Protein synthesis may occur in RNA but not in
DNA.
2. RNA can catalyze (speed up a process) certain
reactions in the form of ribozymes.
3. The enzymatic reduction of RNA nucleotides
enables the synthesis of DNA nucleotides.
Where Did Life Evolve?
- Scientists have found different habitats where
life may have begun. Some of these locations
include soil surfaces, interstellar space, and
even the atmosphere.
- However, soil surfaces would not attract the
quantity of organic material that would be
available in water, whereas stellar space and the
atmosphere are too dry for life to exist.
- Scientists also suggested that life might have
started from the oceans but the complex
organic molecules are vulnerable to damage
due to high sodium and chlorine concentration in
seawater.
- Lakes and seashore lagoons can also be
places where life might have originated because
they have warm temperatures that can promote
chemical reactions; however RNA bases
become increasingly unstable as temperatures
rise above 0 degrees celsius.
- Perhaps the best environment for organic
reactions to occur during early Earth was in cold
volcanic vents.
Origin of Eukaryotic Cells
- Simple prokaryotic organisms are said to be the
ancestors or precursors of eukaryotes.
- Prokaryotes are so successful in an incredible
range of habitats that the can live in swamps,
hindguts of termites, hot springs, and even in
deep sea and underground rocks.
- There are 500 million prokaryotic organism per
liter of ocean water, 1 billion of them per liter of
freshwater and about 300 million bacteria on the
skin of a person. Because there are so many
different kinds of prokaryotes, it is difficult to
search for the possible ancestry of eukaryotes
among them.
- Prokaryotic cells do not possess true nuclei.
- Endosymbiosis is a type of relationship
wherein an organism lives inside its partner.
- According to the endosymbiotic theory,
eukaryotic cells created a symbiotic relationship
with prokaryotic organisms. One group can
produce ATP, and the other can do
photosynthesis.
- Scientists studied DNA structure and ribosomes
and found out that mitochondria and
chloroplasts have many features similar to forms
of free-living bacteria present today.
Multicellularity and Sexual Reproduction
- Most prokaryotes reproduce asexually and
after eukaryotic cells arose, they began to
reproduce sexually.
- The reason behind this far greater speed of
evolution is the shuffling and reshuffling of
genes from one generation to the next.
- Asexual reproduction only produces offspring
that are genetically identical to their parents
while sexual reproduction produces organisms
that never exactly resemble their parents
Paleontology
 - The scientific study of the existence of life,
including the origin and eventual destruction or
extinction of different groups of organisms.
- It is a science that incorporates different
disciplines such as biology, geology, ecology,
archaeology and even computer science to
study the evolution of organisms and how they
interact with the environment.
Paleontologists
- Specialize in studying the ecologies of the
past and the evolution of the organisms that
thrived in these ecologies through careful
observation and documentation of fossils.
- They work to identify the forms of life that
existed millions of years ago
- Archaeopteryx lithographica is from the late
Jurassic and Archaeopteryx is said to have
many features of dinosaurs which provide a
strong evidence of the dinosaur ancestry of
birds.
Geology
- The study of life on Earth based on the
evidence found on rocks.
Geologists
- Scientists who carefully study the different
materials that make up Earth.
- They work to understand the history of Earth by
focusing on the changes of Earth in relation to
changes in climate and land formation.
- They specifically investigate rock formations and
even fossils to measure different physical
properties of Earth.
Paleontologists vs. Geologists
- Paleontologists look at the fossil remains of
different types of organisms beneath the
surface of the Earth to study primitive life.
- Geologists study the outer layer of Earth’s
crust to understand the history of Earth.
- They both work together to understand the
history and evolution of Earth and they both use
the geologic time scale to divide Earth’s
history into time intervals.
Geologic Timescale
- Used to present evolutionary time.
- Shows significant events in the history of Earth
and of the evolution of living things.
- This was developed by scientists by studying
rock layers and index fossils worldwide.
- Other techniques such as radioactive and
relative dating were also used to mark the start
and the end of a segment of geologic time.
- Geologic divisions vary in duration by several
millions of years.
Eons
- Largest divisions in the geologic
timeline.
➔ Phanerozoic eon
- Began more than 500 million years
-Characterized by the existence of
organisms that had skeletons or hard
shells.
➔ Proterozioc eon
- 2.5 billion years ago to 540 million years
ago.
- Where the first multicellular organisms
arose and where mass extinction
occurred.
➔ Archaeozoic eon
- 3.9 to 2.5 billion years ago
- Where the first life-forms represented by
single-celled organisms appeared
➔ Hadean eon
- 4.6 to 3.9 billion years ago
- Characterized by Earth’s formation from
dust and gases.
The Proterozoic, Archaeozoic, and the Hadean eons are
sometimes collectively known as the Precambrian time
which accounts for almost 90% of Earth’s history.
Eras
- Smaller intervals of an eon
➔ Paleozoic era
- Began 540 million years ago
- Where fossil records became rich with
evidence of many marine organisms
➔ Mesozoic era
- Began about 200 million years ago and
lasted for about 180 million years.
- Called as the Age of Reptiles or the Age
of Dinosaurs because this is when many
kinds of dinosaurs existed.
- Also marked by the appearance of
flowering plants.
➔ Cenozoic era
- Latest era in the geologic timeline
- Began from 65 million years ago up to
the present
- Composed of the quaternary and tertiary
periods
- Characterized by the presence of
primitive mammals and modern human
civilization
- Sometimes called as the Age of
Mammals
Periods
- Further subdivisions of eras.
Legend : Periods behind the arow are the periods while
the eras in parenthesis beside are the respective eras
they belong under.
➔ Vendian/Ediacaran (Proterozoic eon)
- Where prokaryotic organisms began to
appear.
- Life in this period only thrived in
underwater and only a few fossils
existed because animals were all soft-
bodied.
 ➔ Cambrian Period (Paleozoic era)
- Organisms were noted to have hard
body parts such as shells and outer
skeletons.
- Brachiopods are also common in this
era which were small animals with two
shells.
- Trilobites were the most dominant
macroscopic life-forms in this period.
➔ Ordovician and Silurian Period (Paleozoic
Era)
- Early forms of cephalopods (include
octopi and squids appeared)
- Vertebrates or animals with backbones
first appeared in this period in the form
of jawless fishes which had suckerlike
mouths.
- Invertebrates or animals without
backbones first appeared in this period
in the form of an insect.
- Land plants also appeared in this
period.
➔ Devonian Period (Paleozoic Era)
- Many plants, including ferns adapted to
drier areas which allowed them to
invade other kinds of habitats.
- Aquatic areas on the other hand were
mostly populated with both invertebrates
and vertebrates.
- Referred to as Age of the Fishes.
- Sharks appeared in the later part of this
period.
➔ Carboniferous and Permian Periods
(Paleozoic Era)
- Reptiles evolved from amphibians.
- Winged insects, giant ferns and other
plants formed vast swampy forests.
- The remains of ancient plants formed
thick deposits of sediments that
changed into coal
At the end of the Paleozoic era, many organisms
became extinct due to the mass extinction where as
much as 95% of complex life-forms in the oceans
disappeared. Those who survived this included reptiles
and groups of fishes.
➔ Triassic Period (Mesozoic Era)
- About 225 million years ago, the first
dinosaurs appeared.
- Coelophysis are meat-eaters that had
light, hollow bones to help them run
swiftly on their hind legs
- Mammals during this period were small
➔ Jurassic Period (Mesozoic Era)
- Dinosaurs became the dominant
animals on land for about 150 million
years.
- Dicraeosaurus was one of the largest
dinosaurs in this period.
-Archaeopteryx made paleontologists
believe that birds are close relatives of
dinosaurs.
➔ Cretaceous Period (Mesozoic Era)
- When reptiles were dominant
vertebrates on Earth.
- Several kinds of birds began to exist.
- Pterosaurs (flying reptiles)
- Iguanodon and Triceratops are species
that emerged as common herbivores
- Tyrannosaurus rex and Spinosaurus
were some of the dominant carnivores
in this period.
- Aquatic organisms like rays, sharks,
corals, and sea stars as well as marine
reptiles dominated the waters
- Angiosperms or flowering plants also
arose in this period
- Ended with a meteorite-caused mass
extinction
➔ Tertiary Period (Cenozoic Era)
- From 65 to 1,8 million years
- Started with emergence of primitive
mammals
- Earth’s climate was warm and mild in
this period.
- Grasses emerged providing a vital food
source
- Marine mammals such as dolphins and
whales thrived.
- Flowering plants and insects flourished.
➔ Quaternary Period (Cenozoic Era)
- Coined as the “Age of Man”
- 1.8 million years ago up to the present.
- Characterized by a series of ice ages
followed by warmer climates.
- At the start of this period, thick
continental glaciers were present in
Europe and North America
- When earth began to warm up (20 000
years ago) the glaciers melted which
resulted in an increase sea level.
- Organisms that thrived included : algae,
corals, mollusks, fishes, sea mammals,
bats, cats, dogs, cattle, and mammoths
- This period is where hominids also
appeared which is believed to be the
ancestors of our species (humans).
- Modern humans Homo sapiens might
have followed might have evolved as
early as 100 000 years ago in Africa.
- From there, the began a series of
migration resulting in human
colonization of the world.
Epochs
- Finer subdivisions shown in the Cenozoic era
and parts of the Mesozoic era.
- Only done for the most recent portion of the
geologic time scale because old rocks in the late
portions of the timescale have been buried
deeply, causing them to be intensely deformed
and severely modified by long-term Earth
processes.