MBD Lec Midterms

MOLECULAR BIOLOGY AND DIAGNOSTICS
LECTURE | PROFESSOR: MA. CLARIZ ISABELLE MAGLALANG
MODULE 1: INTRODUCTION TO MOLECULAR BIOLOGY AND DIAGNOSTICS
HISTORY
● Griffith used heat to kill the S strain bacteria, and he
A. BACTERIAL TRANSFORMATION then injected these dead bacteria into the third group of
FREDERICK GRIFFITH (1928) mice. So, the mice injected with this heat-killed S strain
● First to discover bacterial transformation survived as the bacteria were dead.
● Streptococcus pneumoniae ● For the fourth group of mice, he injected the mice with
○ Avirulent = R bacteria (rough coat) the combination (heat-killed S strain and live R strain)
○ Virulent = S bacteria (smooth coat) and the mice injected with this developed pneumonia
and died.
Transformation The transfer of genetic material from one ● On their own, heat-killed S strain and live R strain are
bacteria to another not deadly. So, based on his experiment, Griffith
concluded that the live R strain acquired some type of
Virulence It is determined by its capsular deadly component from the dead S strain.
polysaccharide. ● So itong live R strain is nakainherit sya ng something
deadly from heat-killed S strain. So, natransfer yung
Virulent Avirulent genetic material.
● His work proved that some organisms can acquire new
They are Nonencapsulated properties from their environment and from one another.
encapsulated And also, non heritable exchange of genetic information
which makes it is possible.
hard for the
phagocytic cells
to engulf and B. THE “TRANSFORMING PRINCIPLE”
destroy them AVERY, MacLEOD, AND McCARTY (1944)
● “DNA is the Genetic Material for Bacteria”
● DNA is the transforming substance
GRIFFITH’S EXPERIMENT
● In his experiment, he injected different types of bacterial

strains into a group of mice. First we have the live S
strain and we also have live R strain, and the heat-killed
S strain with the live R strain.
● Mice from group 1 were injected with the virulent S
strain, they then developed pneumonia and died.
● Mice from group 2 who were injected with the ● In their experiment, they also used the S. pneumoniae.
nonvirulent R strain survived. So, most remain healthy. ● There are four major groups of biomolecules:
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○ Carbohydrates ● They were able to label the DNA using the T2

○ Lipids bacteriophage. This bacteriophage were able to infect
○ Proteins the E. coli
○ Nucleic acids ● Hershey and Chase used two groups of bacteriophages
● Scientists before were unsure which was responsible and made a single component radioactive each in order
for inheritance, but they believed it was either the to keep track of what it was doing.
proteins or the nucleic acids. ● In one group, they tested the viral protein coat and in
● The laying ground for this experiment was Griffith’s the other group they tested the nucleic acids in the
work. inside.
● So, using the heat-killed S strain bacteria, they
inactivated various substances. Heat-killed S strain with
the nonvirulent R strain bacteria were mixed with
inactivated proteins and RNA (inactivated meaning NO
protein and NO RNA).
● The R strain still transformed into a deadly S strain.
This then ruled out RNA and proteins as the genetic ● So, once the appropriate molecules were tabbed, the
material. experiment consists of three major steps. We have the
● But when they inactivated DNA in the S strain, the R infection, blending, and centrifugation.
strain did not transform. This led to the conclusion that ● In the infection step, they allow the bacteriophage to
DNA is the genetic material. So, the DNA was also infect a host cell to see whether the radioactive proteins
inactivated but hindi nagtransform yung R strain natin or radioactive nucleic acids will make radioactive
which concludes that DNA is the transforming factor. bacteriophage.
● In the blending step, they use a high speed blender to
C. DNA IS THE GENETIC MATERIAL jiggle the E. coli cells and after shake off the empty
protein coats on the outside. This created a mixture of
ALFRED HERSHEY AND MARTHA CHASE (1953) liquid phage part and bacteria called a suspension.
● Used T2 Bacteriophage to identify whether DNA or ● In the centrifugation step, heavier bacterial cells
proteins is the genetic material condensed into a pellet and settled at the bottom of the
● Used radioactive elements ‘S’ (Sulfur) and P (Phosphorus) tube. Then the lighter cells remain suspended in the
to label protein and DNA liquid called the supernatant.
○ Sulfur - labeled the protein coat ● So, Hershey and Chase then tested the radioactivity in
○ Phosphorus - labeled the genetic material or the the pellets and in the liquid to see where the
nucleic acid radioactivity ended up.
● Proved that DNA is the genetic material ● So, the results of the experiment show that in the
nucleic acid group, the pellet were more radioactive
HERSHEY-CHASE EXPERIMENT
than the supernatant. And in the protein group, the
supernatant was more radioactive than the pellets. This
then concludes that the nucleic acids are the
molecules of inheritance.
D. RNA IS THE GENETIC MATERIAL FOR VIRUSES

● RNA can be used as a genetic material in viruses.
○ This was first demonstrated when purified RNA
from Tobacco mosaic virus was spread in tobacco
leaves.
● Retroviruses
○ These are viruses that are known to use RNA as
their genetic material.
○ They utilize Reverse Transcription to replicate
their genetic material. (So normally ang nagyayare
is we convert DNA to RNA. Now, sa reverse
transcription naman we convert RNA to DNA and
mat-transcribe and RNA ulet.
○ An example of reverse transcription:
■ Human Immunodeficiency Virus (HIV)
BACO | PANTIG
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NUCLEIC ACID
○ Guanine
COMPONENTS OF NUCLEIC ACID
NUCLEOTIDES DNA VS RNA
● Building blocks of nucleic acids
● Composed of 3 subunits To differentiate DNA from RNA, we look for the
○ Pentose Sugar presence of THYMINE and URACIL
○ Phosphate Group ● Thymine can only be found in DNA
○ Nitrogenous Base ● Uracil can only be found in RNA
PENTOSE SUGAR
NUCLEOSIDE
● Has two types:
○ Ribose ● Composed of nucleobase (nitrogenous base), either a
■ C2 has hydroxyl (OH) group pyrimidine or a purine, with a pentose sugar component
○ 2-Deoxyribose ● Basic structure of nucleotide
■ C2 has hydrogen atom ● Nitrogenous Base + Sugar
● Absence of phosphate group
PHOSPHATE GROUP
● Third component of the nucleotide
● Derived from Phosphoric Acid
NUCLEOTIDE FORMATION
NITROGENOUS BASE
PYRIMIDINE
Nucleoside WITHOUT phosphate group
Nucleotide WITH phosphate group
● Monocyclic base with six (6) membered ring

○ Cytosine ERWIN CHARGAFF
○ Uracil ● Austrian-American Biochemist who conceptualized that
○ Thymine the complementary bases are equal:
○ Adenine = Thymine
PURINE ○ Guanine = Cytosine
CHARGAFF’S RULE
1 Two long polynucleotide chains are coiled around a

central axis, forming a right handed double helix
2 The two DNA strands are antiparallel, that is, their 5’

to 3’ orientation runs in opposite directions
3 The base of both chains lie perpendicular to the axis,

and they are stacked on one another
● Bicyclic base with fused five (5) and six (6) membered
ring
4 The nitrogenous bases of opposite chains are paired
○ Adenine
as the result of the formation of a hydrogen bond in
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DNA DNA DOUBLE HELIX
5 Each complete turn of the helix is 34˚ angle long
6 The double helix has a diameter of 20˚ angle
7 The amount of adenine (A) residues is proportional

to the amount of thymine (T) residues in DNA. Also,
the amount of guanine (G) residues is proportional to
the amount of cytosine (C)
8 The sum of the purines is equal to the sum of

pyrimidine
9 The percentage of (G+C) is not necessarily equal

the percentage of (A+T)
DNA
DNA FORMS A DOUBLE HELIX
MAURICE WILKINS & ROSALIND FRANKLIN
● Used X-ray diffraction indicated DNA is a helix
● Rosalind Franklin was introduced to Maurice Wilkins as he
has the technology to visualize the DNA using X-ray
● Rosalind Franklin was the first person to produce a DNA
photograph called Photo 51
JAMES WATSON ● Involves two polynucleotide strands that are coiled

around each other
● James Watson who was having his post-doctoral studies ● Sugar and Phosphate “backbone”
went to Europe and heard about the photo ● Hydrogen bonds hold the two strands together
● He contacted Maurice Wilkins and showed the photo to ● DNA strands are antiparallel (5’ to 3’ and vice versa)
him without the knowledge of Rosalind Franklin
JAMES WATSON AND FRANCIS CRICK HYDROGEN BONDING INTERACTIONS

● James Watson, became intrigued then went back to
America where he met Francis Crick, a physicist
● The two began to construct the DNA model and when
finished, they announced the structure of the DNA in an
article which made them win a Nobel Prize
Image of Watson and Crick elucidating the 3D structure of

DNA (left). Image of photo 51 (right)
● It is the formation of hydrogen bonds between

complementary bases
● It is an important factor in stabilizing the DNA double
helix structure
BACO | PANTIG
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BASE STACKING INTERACTIONS REFERENCES

❖ Shen CH. Diagnostic molecular biology. Academic Press;
2019.
❖ Karp G, Iwasa J, Marshall W. Karp’s Cell and Molecular
Biology. John Wiley & Sons; 2020.
❖ Alberts B, Johnson A, Lewis J, Morgan D, Raff M, Roberts
K, et al. Molecular Biology of the Cell. 2017.
❖ Brown T. Introduction to Genetics: A Molecular Approach.
New York and London: Garland Science, Taylor & Francis
Group, LLC; 2012.
● Gives the staircase appearance of the DNA

structure.
ALTERNATIVE FORMS OF DNA
● These are similar to the normal DNA we know, but

they form in certain types of environments.
A-DNA Observed when DNA is dehydrated or under

high salt concentrations
It is right-handed and turns clockwise
B-DNA Exist under very high humidity environment
It is right-handed and turns clockwise
Z-DNA Formed under high salt or in the presence of

alcohol
Longer and narrower than B-DNA
It is left-handed and turns counterclockwise
BACO | PANTIG
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Molecular Biology and Diagnostics Lecture
Module 2: Amino Acids and Proteins - Humans can synthesize only 10 of the 20 amino acids
needed for proteins. The remaining 10, called essential
PROTEINS amino acids, must be obtained from the diet and
- Came from the Greek word “proteios” meaning “of first consumed on a regular, almost daily basis.
importance”
- 50% of the dry weight of the human body Essential (Kailangan Not synthesized in the
- Proteins are not stored, so they must be consumed daily kainin) body in adequate amts,
- RDI for adults is 0.8 grams of protein per kilogram of body therefore it is ESSENTIAL
weight to consume them
- One of the most important macromolecules Nonessential (Di na Synthesized in the body in
- Broad range of structure and function: kailangan kainin) adequate amts therefore it
is NOT ESSENTIAL to
o Enzymatic
consume them
o Regulatory
o Structural
20 COMMON NATURALLY OCCURING AMINO ACIDS
o Carrier proteins
- Biomolecules that contain many amide bonds formed by
Nonessential Essential
joining amino acids
Alanine Ala A Arginine Arg R
- Amino acids are the building blocks of proteins
Asparagine Asn N
Histidine His H
Aspartic Asp D Isoleucine Ile I
Acid Leucine Leu L
Cysteine Cys C
Lysine Lys K
Glutamine Gln Q
Glutamic Glu E Methionine Met M
Acid
Phenylalanine Phe F
Glycine Gly G
Proline Pro P Threonine Thr T
Serine Ser S Tryptophan Trp W
Tyrosine Tyr Y Valine Val V
Essential amino acids are standard amino acids needed

for protein synthesis that must be obtained from dietary
sources because the human body cannot synthesize it in
adequate amounts from other substances
AMINO ACIDS
STEREOCHEMISTRY OF AMINO ACIDS
- Have two functional groups: amino group (NH2) and
carboxyl group (COOH)
Chirality – refers to mirror images and characteristics of
- The amino group is bonded to the α carbon, the carbon
non-superimposability (left and right hand)
adjacent to the carbonyl group, making them 𝛂-amino
acids.
All amino acids except GLYCINE have a chirality center
- R group (side chain) determines the identity of amino acids,
on the alpha carbon (a carbon bonded to FOUR
i.e., whether it is an acidic or basic amino acid
DIFFERENT GROUPS on the alpha carbon)
o Amino acids with an additional COOH group in the
side chain are called acidic amino acids
L Amino acids have the –NH3 + group on the left side in
o Those with an additional basic N atom in the side
the Fischer projection. Common naturally occurring amino
chain are called basic amino acids.
acids are L isomers.
o All others are neutral amino acids.
o L for Levorotatory/ Laevus
R = basic N atom Basic amino acid
D Amino acids have the –NH3 + group on the right side
R = additional COOH group Acidic amino acid
in the Fischer projection. D Amino acids occur infrequently
in nature.
- Glycine is the simplest amino acid
o D for Dextrorotatory/ Dexter
- All amino acids have common names, which are
abbreviated by a three-letter or one-letter designation.
PEPTIDES
- There are 20 kinds of amino acids which are at ones alike
- Short chains of amino acids joined together by peptide
and dissimilar
bonds
o They share common features that would allow
- Peptide bonds or amide bonds
them to form peptide bonds with each other but at
- The amide bonds in peptides and proteins are called
the same time they have a distinctive chemical
peptide bonds
features and that diversity of amino acids, and
- The individual amino acids are called amino acid residues.
possible number of combinations they can have
allows for dissimilarities.
- A dipeptide has two amino acids joined together by one used for the β-pleated sheet. These representations are often
amide bond used in ribbon diagrams to illustrate protein structure.
- A tripeptide has three amino acids joined together by two
amide bonds
- Polypeptides and proteins both have many amino acids
joined together in long linear chains, but the term protein is
usually reserved for polymers of more than 40 amino
acids.
STRUCTURE OF PROTEINS
TERTIARY STRUCTURE
PRIMARY STRUCTURE - The three-dimensional shape adopted by the entire peptide
- The primary structure of a protein is the particular sequence chain
of amino acids that is joined together by peptide bonds. - 3D arrangement of localized regions of proteins
- SIMPLEST - These regions arise due to hydrogen bonding between the
- All bond angles are 120° and the C-O double bonds and N- N-H group of one amide with the C=O group of another
H single bonds are oriented 180° from each other. As a - Produced by interactions between amino acid residues that
result, the backbone of the protein adopts a zigzag may be located at considerable distance from each other in
arrangement. the primary sequence of the polypeptide chains
Disulfide bonds Strongest Form covalent bond to stabilize

interaction the tertiary structure
Electrostatic “Salt Amino acids with charged side

interactions Bridges” chains are attracted
SECONDARY STRUCTURE
- Includes various types of local conformations. These are Hydrogen bonds Weak and Occur between polar functional
formed by regular repeating pattern of hydrogen bond easily groups
formation between backbone atoms disrupted
- Two arrangements that are particularly stable are called the London Weakest Occur between hydrophobic
dispersion forces bond groups which stabilizes the
𝛂-helix and the 𝛃-pleated sheet.
structure
Alpha Helix
- The 𝛂-helix forms when a peptide chain twists into a right- Interactions between the residues that can produce the 3D
handed or clockwise spiral (e.g., myosin shape of the protein:
and 𝛂-keratin - Hydrophobic interaction
o Each turn of the helix has 3.6 - Electrostatic interaction
amino acids - Hydrogen bonds
o The N-H and C=O bonds point - London dispersion forces
along the axis of the helix in - Covalent disulfide bonds
opposite directions.
o The C=O group of one amino acid QUATERNARY STRUCTURE
is hydrogen bonded to an N-H - Refers to the spatial arrangement of subunits in a protein
group four amino acid residues that consists of more than one polypeptide chain
farther along the chain
o The R groups of the amino acids PROTEIN DENATURATION
extend outward from the core of the helix. - Alters the shape of the protein
- Denaturation is a process of altering the shape of a protein
Beta Pleated Sheet without breaking (hydrolysis) the amide bonds that
- The 𝛃-pleated sheet forms when two or more peptide form the primary structure/ without changing the AA
chains, called strands, line up side-by side. sequence
- Examples: Heat (unfolding without causing hydrolysis of
Super Secondary Structure peptide bonds) and Urea; high temperature, acid, base,
agitation can disrupt the non-covalent interactions that hold
Shorthand symbols, called ribbon diagrams, are used to a specific protein in a specific shape
indicate these regions of secondary structure. - Destroys SECONDARY AND TERTIARY structure
- Denaturation often makes globular proteins LESS WATER
Most proteins have regions of α-helix and β-pleated sheet, in SOLUBLE
addition to other regions that cannot be characterized by either o Solubility of a protein depends on its 3D shape
of these arrangements. Shorthand symbols are often used to o Globular proteins are more soluble than fibrous
indicate these regions of secondary structure, as well as proteins
disulfide bonds that are sometimes present. In particular, a flat Denaturation makes globular proteins not
helical ribbon is used for the α-helix, while a flat wide arrow is so globular anymore
Module 3:
The Central Dogma
CENTRAL
DOGMA
DNA RNA
genetic
-> information / genes transcribes
->
a regulates genes
-> Nitro bases:Cytosine, Guanine, Nitro bases:same
->
except thymine ->
Thymine, Adenine Uracil
sugar:Deoxyribose sugar:Ribose
->
->
messenger RNA (mRNA) - brings the information from the DNA in the nucleus
↳ brings info from nucleus to to the protein manufacturing area, the cytoplasm.
protein manufacturing area, the The mRNA becomes the template of information to
cytoplasm
make proteins.
↳ mRNA:template for protein
synthesis
ribosomal RNA (rRNA) - hold tightly into the mRNA using its information to
↳ holds mRNA assemble the amino acids in correct order
↳ arranges amino acids into
correct order
transfer RNA (tRNA) - supplies amino acids to the ribosome to be

supplies amino acids to
assembled as protein
->
the ribosome
a.d.
->
assembled into protein
Central Dogna
Replication
DNA is replicated.
->
Transcription
DNA
->
to RNA.
Translation
RNA to proteins,
->
Replication ① DNA molecule is unzipped
parent
② sequence of bases exposed
③ these bases serve as
template
2 insertion of complementary bases on synthesized strand
As the hydrogen bonds between the base pairs are

broken, DNA replication starts with the unzipping of
the parent molecule. The sequence of bases on each
of the separated strands, once exposed, serves as a
template to direct the insertion of a complementary
collection of bases on the synthesized strand.
Enzymes involved in DNA replication
Helicase Primase DNA Polymerase Ligase

Unwinds and adds short binds joins the Okazaki
separates primer to nucleotides to fragments together
strands template strand form new into a single DNA
strands molecule
Helicase Primase DNApolymerase Ligase

unwind
-> sep avate or
adds short
->
->binds nucleotides
joins Okazaki
->
strands form new strands

to
fragments together
template
strands to
into 1 molecule
DHA -> RNA
RNA -
protein
This page has been archived and is no longer updated
NUCLEIC ACID STRUCTURE AND FUNCTION | Lead Editor: Bob Moss
Translation: DNA to mRNA to Protein

By: Suzanne Clancy, Ph.D. & William Brown, Ph.D. (Write Science Right) © 2008 Nature Education
Citation: Clancy, S. & Brown, W. (2008) Translation: DNA to mRNA to
Protein. Nature Education 1(1):101
How does the cell convert DNA into working proteins? The process of translation can be seen as the
decoding of instructions for making proteins, involving mRNA in transcription as well as tRNA.
Aa Aa Aa
The genes in DNA encode protein molecules, which are the "workhorses" of the cell, carrying out all the functions necessary for life. For example, enzymes, including those
that metabolize nutrients and synthesize new cellular constituents, as well as DNA polymerases and other enzymes that make copies of DNA during cell division, are all
proteins.
In the simplest sense, expressing a gene means manufacturing its corresponding protein, and this multilayered process has two major steps. In the first step, the information
in DNA is transferred to a messenger RNA (mRNA) molecule by way of a process called transcription. During transcription, the DNA of a gene serves as a template for
complementary base-pairing, and an enzyme called RNA polymerase II catalyzes the formation of a pre-mRNA molecule, which is then processed to form mature mRNA
(Figure 1). The resulting mRNA is a single-stranded copy of the gene, which next must be translated into a protein molecule.
https://www.nature.com/scitable/topicpage/translation-dna-to-mrna-to-protein-393/ 2/21/23, 22:46

Page 1 of 8
Figure 1: A gene is expressed through the processes of transcription and translation.
During transcription, the enzyme RNA polymerase (green) uses DNA as a template to produce a pre-mRNA transcript (pink).
The pre-mRNA is processed to form a mature mRNA molecule that can be translated to build the protein molecule
(polypeptide) encoded by the original gene.
© 2013 Nature Education All rights reserved.
Figure Detail
During translation, which is the second major step in gene expression, the mRNA is "read" according to the genetic code, which relates the DNA sequence to the amino acid
sequence in proteins (Figure 2). Each group of three bases in mRNA constitutes a codon, and each codon specifies a particular amino acid (hence, it is a triplet code). The
mRNA sequence is thus used as a template to assemble—in order—the chain of amino acids that form a protein.

Page 2 of 8
Figure 2: The amino acids specified by each mRNA codon. Multiple codons can
code for the same amino acid.
The codons are written 5' to 3', as they appear in the mRNA. AUG is an initiation codon;
UAA, UAG, and UGA are termination (stop) codons.
Figure Detail
But where does translation take place within a cell? What individual substeps are a part of this process? And does translation differ between prokaryotes and eukaryotes? The
answers to questions such as these reveal a great deal about the essential similarities between all species.
Where Translation Occurs

Within all cells, the translation machinery resides within a specialized organelle called the ribosome. In eukaryotes, mature mRNA molecules must leave the nucleus and travel
to the cytoplasm, where the ribosomes are located. On the other hand, in prokaryotic organisms, ribosomes can attach to mRNA while it is still being transcribed. In this
situation, translation begins at the 5' end of the mRNA while the 3' end is still attached to DNA.
In all types of cells, the ribosome is composed of two subunits: the large (50S) subunit and the small (30S) subunit (S, for svedberg unit, is a measure of sedimentation
velocity and, therefore, mass). Each subunit exists separately in the cytoplasm, but the two join together on the mRNA molecule. The ribosomal subunits contain proteins and
specialized RNA molecules—specifically, ribosomal RNA (rRNA) and transfer RNA (tRNA). The tRNA molecules are adaptor molecules—they have one end that can read the
triplet code in the mRNA through complementary base-pairing, and another end that attaches to a specific amino acid (Chapeville et al., 1962; Grunberger et al., 1969). The
idea that tRNA was an adaptor molecule was first proposed by Francis Crick, co-discoverer of DNA structure, who did much of the key work in deciphering the genetic code
(Crick, 1958).
Within the ribosome, the mRNA and aminoacyl-tRNA complexes are held together closely, which facilitates base-pairing. The rRNA catalyzes the attachment of each new
amino acid to the growing chain.
The Beginning of mRNA Is Not Translated

Interestingly, not all regions of an mRNA molecule correspond to particular amino acids. In particular, there is an area near the 5' end of the molecule that is known as the
untranslated region (UTR) or leader sequence. This portion of mRNA is located between the first nucleotide that is transcribed and the start codon (AUG) of the coding region,
and it does not affect the sequence of amino acids in a protein (Figure 3).
So, what is the purpose of the UTR? It turns out that the leader sequence is important because it contains a ribosome-binding site. In bacteria, this site is known as the Shine-
Dalgarno box (AGGAGG), after scientists John Shine and Lynn Dalgarno, who first characterized it. A similar site in vertebrates was characterized by Marilyn Kozak and is
thus known as the Kozak box. In bacterial mRNA, the 5' UTR is normally short; in human mRNA, the median length of the 5' UTR is about 170 nucleotides. If the leader is
long, it may contain regulatory sequences, including binding sites for proteins, that can affect the stability of the mRNA or the efficiency of its translation.

Page 3 of 8
Figure 3: A DNA transcription unit.
A DNA transcription unit is composed, from its 3' to 5' end, of an RNA-coding region (pink rectangle) flanked by a promoter
region (green rectangle) and a terminator region (black rectangle). Regions to the left, or moving towards the 3' end, of the
transcription start site are considered \"upstream;\" regions to the right, or moving towards the 5' end, of the transcription start
site are considered \"downstream.\"
© 2014 Nature Education Adapted from Pierce, Benjamin. Genetics: A Conceptual Approach, 2nd ed. All rights reserved.
Translation Begins After the Assembly of a Complex Structure
The translation of mRNA begins with the formation of a complex on the mRNA (Figure 4). First, three initiation factor proteins (known as IF1, IF2, and IF3) bind to the small
subunit of the ribosome. This preinitiation complex and a methionine-carrying tRNA then bind to the mRNA, near the AUG start codon, forming the initiation complex.

Page 4 of 8
Figure 4: The translation initiation complex.
When translation begins, the small subunit of the ribosome and an initiator tRNA molecule assemble on the mRNA transcript.
The small subunit of the ribosome has three binding sites: an amino acid site (A), a polypeptide site (P), and an exit site (E).
The initiator tRNA molecule carrying the amino acid methionine binds to the AUG start codon of the mRNA transcript at the
ribosome’s P site where it will become the first amino acid incorporated into the growing polypeptide chain. Here, the initiator
tRNA molecule is shown binding after the small ribosomal subunit has assembled on the mRNA; the order in which this
occurs is unique to prokaryotic cells. In eukaryotes, the free initiator tRNA first binds the small ribosomal subunit to form a
complex. The complex then binds the mRNA transcript, so that the tRNA and the small ribosomal subunit bind the mRNA
simultaneously.

Page 5 of 8
Figure Detail
Although methionine (Met) is the first amino acid incorporated into any new protein, it is not always the first amino acid in mature proteins—in many proteins, methionine is
removed after translation. In fact, if a large number of proteins are sequenced and compared with their known gene sequences, methionine (or formylmethionine) occurs at the
N-terminus of all of them. However, not all amino acids are equally likely to occur second in the chain, and the second amino acid influences whether the initial methionine is
enzymatically removed. For example, many proteins begin with methionine followed by alanine. In both prokaryotes and eukaryotes, these proteins have the methionine
removed, so that alanine becomes the N-terminal amino acid (Table 1). However, if the second amino acid is lysine, which is also frequently the case, methionine is not
removed (at least in the sample proteins that have been studied thus far). These proteins therefore begin with methionine followed by lysine (Flinta et al., 1986).
Table 1 shows the N-terminal sequences of proteins in prokaryotes and eukaryotes, based on a sample of 170 prokaryotic and 120 eukaryotic proteins (Flinta et al., 1986). In
the table, M represents methionine, A represents alanine, K represents lysine, S represents serine, and T represents threonine.
Table 1: N-Terminal Sequences of Proteins
N-Terminal Percent of Percent of

Sequence Prokaryotic Proteins Eukaryotic Proteins
with This Sequence with This Sequence
MA* 28.24% 19.17%
MK** 10.59% 2.50%
MS* 9.41% 11.67%
MT* 7.65% 6.67%
* Methionine was removed in all of these proteins
** Methionine was not removed from any of these proteins
Once the initiation complex is formed on the mRNA, the large ribosomal subunit binds to this complex, which causes the release of IFs (initiation factors). The large subunit of
the ribosome has three sites at which tRNA molecules can bind. The A (amino acid) site is the location at which the aminoacyl-tRNA anticodon base pairs up with the mRNA
codon, ensuring that correct amino acid is added to the growing polypeptide chain. The P (polypeptide) site is the location at which the amino acid is transferred from its tRNA
to the growing polypeptide chain. Finally, the E (exit) site is the location at which the "empty" tRNA sits before being released back into the cytoplasm to bind another amino
acid and repeat the process. The initiator methionine tRNA is the only aminoacyl-tRNA that can bind in the P site of the ribosome, and the A site is aligned with the second
mRNA codon. The ribosome is thus ready to bind the second aminoacyl-tRNA at the A site, which will be joined to the initiator methionine by the first peptide bond (Figure 5).
Figure 5: The large ribosomal subunit binds to the small

ribosomal subunit to complete the initiation complex.
The initiator tRNA molecule, carrying the methionine amino acid
that will serve as the first amino acid of the polypeptide chain, is
bound to the P site on the ribosome. The A site is aligned with the
next codon, which will be bound by the anticodon of the next
incoming tRNA.

Page 6 of 8
The Elongation Phase
The next phase in translation is known as the elongation phase (Figure 6). First, the ribosome moves along the mRNA in the 5'-to-3'direction,
which requires the elongation factor G, in a process called translocation. The tRNA that corresponds to the second codon can then bind to the
A site, a step that requires elongation factors (in E. coli, these are called EF-Tu and EF-Ts), as well as guanosine triphosphate (GTP) as an
energy source for the process. Upon binding of the tRNA-amino acid complex in the A site, GTP is cleaved to form guanosine diphosphate
(GDP), then released along with EF-Tu to be recycled by EF-Ts for the next round.
Next, peptide bonds between the now-adjacent first and second amino acids are formed through a peptidyl transferase activity. For many
years, it was thought that an enzyme catalyzed this step, but recent evidence indicates that the transferase activity is a catalytic function of
rRNA (Pierce, 2000). After the peptide bond is formed, the ribosome shifts, or translocates, again, thus causing the tRNA to occupy the E site.
The tRNA is then released to the cytoplasm to pick up another amino acid. In addition, the A site is now empty and ready to receive the tRNA
for the next codon.
This process is repeated until all the codons in the mRNA have been read by tRNA molecules, and the amino acids attached to the tRNAs
have been linked together in the growing polypeptide chain in the appropriate order. At this point, translation must be terminated, and the
Figure 6
nascent protein must be released from the mRNA and ribosome.
Figure Detail
Termination of Translation
There are three termination codons that are employed at the end of a protein-coding sequence in mRNA: UAA, UAG, and UGA. No tRNAs recognize these codons. Thus, in
the place of these tRNAs, one of several proteins, called release factors, binds and facilitates release of the mRNA from the ribosome and subsequent dissociation of the
ribosome.
Comparing Eukaryotic and Prokaryotic Translation

The translation process is very similar in prokaryotes and eukaryotes. Although different elongation, initiation, and termination factors are used, the genetic code is generally
identical. As previously noted, in bacteria, transcription and translation take place simultaneously, and mRNAs are relatively short-lived. In eukaryotes, however, mRNAs have
highly variable half-lives, are subject to modifications, and must exit the nucleus to be translated; these multiple steps offer additional opportunities to regulate levels of protein
production, and thereby fine-tune gene expression.
References and Recommended Reading

Chapeville, F., et al. On the role of soluble ribonucleic acid in coding for amino acids. Proceedings of the National Academy of Sciences 48, 1086–1092 (1962)
Crick, F. On protein synthesis. Symposia of the Society for Experimental Biology 12, 138–163 (1958)
Flinta, C., et al. Sequence determinants of N-terminal protein processing. European Journal of Biochemistry 154, 193–196 (1986)
Grunberger, D., et al. Codon recognition by enzymatically mischarged valine transfer ribonucleic acid. Science 166, 1635–1637 (1969) doi:10.1126/science.166.3913.1635
Kozak, M. Point mutations close to the AUG initiator codon affect the efficiency of translation of rat preproinsulin in vivo. Nature 308, 241–246 (1984) doi:10.1038308241a0
(link to article)
---. Point mutations define a sequence flanking the AUG initiator codon that modulates translation by eukaryotic ribosomes. Cell 44, 283–292 (1986)
---. An analysis of 5'-noncoding sequences from 699 vertebrate messenger RNAs. Nucleic Acids Research 15, 8125–8148 (1987)
Pierce, B. A. Genetics: A conceptual approach (New York, Freeman, 2000)
Shine, J., & Dalgarno, L. Determinant of cistron specificity in bacterial ribosomes. Nature 254, 34–38 (1975) doi:10.1038/254034a0 (link to article)
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APPLICATIONS IN BIOTECHNOLOGY DISCOVERY OF GENETIC MATERIAL
Genetically Modified Organisms (GMOs): Barbara McClintock and the Discovery of

Transgenic Crops and Recombinant DNA Jumping Genes (Transposons)

Page 7 of 8
Because DNA is stable, it makes a great medium for storage of genetic info.
It's like a hard-drive, or a reference book.
RNA is more reactive and will break-down spontaneously, so it is not a

great storage medium, but it is an excellent tool for transferring info or for
chemical reactions.
There are a bunch of other forms of RNA which are possible because RNA is
reactive and very adaptable.
mRNAa arranges in correctorder
↑ holds
a.a.
The most abundant form of RNA is ribosomal (rRNA), which is used to

produce all the proteins in your body. The other common RNA is
messenger RNA (mRNA), commonly understood to be the short-term
transfer medium for genetic info.
Thank you!
LECTURE | PROFESSOR: ISABELLE MAGLALANG
MODULE 5: GENE EXPRESSION: TRANSCRIPTION OF THE GENETIC CODE
GENE EXPRESSION
TYPES OF NUCLEIC ACID
● Process to produce a functional product
○ Such as a polypeptide ● We have two types of nucleic acids, namely the DNA
● Along with the environmental factors, the molecular and RNA
expression of genes determines an organism’s trait. For a
gene to be expressed, few different types of sequences
perform specific rules. For example, the promoter and
terminator are base sequences used during transcription
○ Promoter
■ This provides a site to begin transcription
○ Terminator
■ This specifies the end of transcription
NOTE: These two sequences cause RNA synthesis to occur

within a defined location.
RECAP: CENTRAL DOGMA
DEOXYRIBONUCLEIC ACID (DNA)

● Usually double-stranded
● Thymine as the base and deoxyribose as the sugar
● It maintains protein encoding information and this
cannot function as an enzyme
RIBONUCLEIC ACID (RNA)

● Usually single-stranded
● Uracil as the base and ribose as the sugar
● It carries protein encoding information and controls how
information is used and this can function as an
enzyme
● We have here a DNA which is replicated (replication). It MAJOR TYPES OF RNA

will then be transcribed (transcription) to RNA. So, from
thymine, it became uracil.
● The RNA now goes to the cytoplasm, specifically in the
endoplasmic reticulum. RNA will bind to rough ER, and
after that the protein will be produced.
● After the production of protein, modification and
corrections of the structure of proteins will occur
● As we know, proteins must be correctly and properly
structured to be functional.
● We have three major types of RNA, namely mRNA,
rRNA, and tRNA
MESSENGER RNA ( MRNA)

● Encodes the amino acid sequence
● Brings in the DNA instructions
BACO | CASTRO | DIMALANTA | PANTIG | PRADO

AUF BSMT 3B & F 1
TRANSFER RNA ( TRNA) ○ Small subunit – 1,900 RNA bases

● Transports specific amino acids to the ribosome for
protein synthesis TRANSFER RNA (tRNA)
● Brings amino acids
RIBOSOMAL RNA ( RRNA)

● Associated with proteins to form ribosomes
● Actually used to support or it can also catalyze protein
synthesis
● The site for protein synthesis
MESSENGER RNA (mRNA)
● Has a clover-like shape

● It has three (3) hairpin loops that act as recognition
sites for anticodon binding.
TRANSCRIPTION
● Carries the genetic information that comes from the
DNA and it is produced by means of transcription
○ Eukaryotes – mRNA is produced inside of the
nucleus
○ Prokaryotes – mRNA is produced inside the
cytoplasm
● It is transported to the ribosome because the ribosome
will be the site for protein synthesis
● There are three nucleotides present in the mRNA which
are called the “codon” which specifies the type of
protein that will be produced
● For the parts:
○ mRNA – which has the instruction coming from
● Basic mechanism for gene expression
DNA
● It involves three steps:
○ Assembled rRNA – we call this now ribosome. It is
○ Initiation
assembled because we have the large subunit and
○ Elongation or synthesis of RNA transcript
the small subunit that organize during protein
○ Termination
synthesis
● The 3 steps involve protein to DNA interaction
○ Anticodon - transported by the transfer RNA
(tRNA).
RIBOSOMAL RNA (rRNA)
● This will organize into ribosomes and it will become the

site for protein synthesis
● rRNA also provides structural support and catalysis. This illustration shows a double-stranded DNA. What
Example would be the enzyme “ribozyme” also known happens here is that the double-stranded DNA unwinds and
as ribonucleic acid enzyme that helps to synthesize the then the RNA Polymerase binds. Once the RNA polymerase
peptide bond in amino acids. binds, it synthesizes the RNA from 3’ to 5’ direction.
● As seen in the illustration above, the large subunit (red
arrow) and small subunit (green arrow) organize only
during protein synthesis. They only differ on the number
of RNA bases:
○ Large subunit – 5,080 RNA bases

AUF BSMT 3B & F 2
STEP 1: INITIATION ○ Contains a gene that codes for a single polypeptide

which is the RNA polymerase
● RNA polymerase
○ Responsible for transcribing all of the different
kinds of RNA or at least the three (3) major types in
bacterial cell
INITIATION
● It is the recognition stage that would be started by the

transcription factor (TF).
● The sequences under or within the promoter region are
recognized by TF.
● TF will enable the RNA polymerase to bind with the
promoter
STEP 2: ELONGATION
● Once the initiation takes place, when the RNA

polymerase binds to the promoter, thereby positioned at
the start of transcription. When this happens, it is
possible to start growing the RNA molecule by
elongation
● A series of cyclic reactions occur during which an RNA
is produced beginning at the 5’ end of the RNA growing
towards the 3’ end.
● Sigma Factor
STEP 3: TERMINATION
○ Recognize the promoter and influences the
function of RNA polymerase
● RNA Polymerase Holoenzyme
○ Initiates the transcription
○ After it is assembled into its 6 subunits, it binds
loosely to the DNA and slides along it
○ This holoenzyme encounters a promoter sequence
then the sigma factor recognizes the bases at both
● As elongation continues, it reaches the termination the -35 and -10 regions
stage. ○ Hydrogen binding occurs between the nucleotides
● The RNA polymerase reaches the termination site at at the -35 and -10 regions of the promoter and then
which the RNA is freed up or released amino acid side chains in the helix turn helix
structure of the sigma factor
TRANSCRIPTION: ○ The helix turn helix motif structure binds tightly to
PROKARYOTES VS EUKARYOTES the regions of -35 and -10 of the promoter
● Only when the sigma factor within the holoenzyme
PROKARYOTES binds to the promoter region to form the closed
complex. Transcription will be then be initiated
● Transcription will start when the double-stranded DNA
unwinds into an open complex (from closed to open)
○ RECALL: Adenine and thymine have 2 hydrogen
bonds and they are easily separated because they
are weaker than cytosine and guanine
● In an open complex, a short RNA strand will be formed,
then the sigma factor will be released from the core
enzyme and once released, it will now signify the start
of the elongation stage. Core enzyme will slide in RNA
to synthesize it
● Catalyzed by a single RNA polymerase
● Escherichia coli
ELONGATION

AUF BSMT 3B & F 3
RHO DEPENDENT TERMINATION

● Rho (ρ) is responsible for terminating transcription for
● At this stage, the RNA transcript is made
certain genes
○ DNA strand is used as template strand or also
● For this termination, the process requires 2
known as antisense strand
components:
○ While the opposite strand is the coding or sense
○ Rho utilization site (“rut”)
strand. It has the same coding as your RNA
■ Sequence upstream from the terminator
transcript
■ This site acts as a recognition site for the
● In RNA synthesis, only the template strand is used and
binding of Rho proteins
the coding strand is never used
■ Rho proteins functions as helicases that
● As your RNA polymerase moves along the DNA, the
separates the RNA from the RNA-DNA hybrid
open complex is formed 17 base pairs long
regions
● Behind this open complex, the DNA rewinds back to its
■ After this site is synthesized in the RNA, Rho
double helix
proteins will now bind sa RNA and will move to
● RNA polymerase always connects the nucleotides in a
the direction of the RNA polymerase
5’ to 3’ region
○ Site where the termination actually occurs
● As RNA polymerase move, rewinding of DNA occur
■ In this site, DNA encodes RNA sequences
containing several guanine to cytosine base
TERMINATION pairs. They form the stem loop
■ This results in the conformational changes that
● Hydrogen bonds between the DNA and RNA within the will cause the RNA polymerase to pause its
open complex prevents the dissociation of the RNA synthesis of RNA
polymerase from the template strand ■ This will allow the Rho proteins to catch up and
● When short RNA-DNA hybrid is forced to separate, then break the hydrogen bonds between the DNA
termination occurs and RNA within the open complex.
● This releases the RNA polymerase and the newly made ■ The completed RNA during the transcription will
RNA transcript now separated from the DNA along with the
● In Escherichia coli, we have two different mechanisms RNA polymerase
of termination:

AUF BSMT 3B & F 4
RHO INDEPENDENT TERMINATION ● Again, if the lactose is present in the cell, it will bind to
the repressor, resulting in an inactive repressor (lactose
● Intrinsic Termination
bound to the repressor)
● Does not require Rho protein
○ This repressor will not be able to bind to the
● The terminator is composed of two adjacent nucleotide
operator because it cannot fit
sequences that function in the RNA
● If the repressor can no longer bind to the repressor, the
○ First Sequence: Uracil Rich Sequence on 3’ end
RNA polymerase can synthesize the RNA for these
○ Second Sequence: Adjacent to the Uracil Rich
enzymes to be synthesize
Sequence and promote the formation of stem loop
● If these enzymes are synthesized, they will metabolized
structure
the lactose, including the lactose bound to the repressor
■ Stem loop structure is important in the
● Once the lactose bound to the repressor is metabolized,
termination step of bacteria
the repressor can now fit to the operator, causing the
■ The formation of stem loop causes the pause of
RNA polymerase synthesis to stop.
the RNA polymerase that synthesizes RNA
■ Thus, if stem loop is present, transcription will
automatically pause EUKARYOTES
■ At the time that RNA polymerase will pause, the
Uracil Rich Sequences in the RNA transcript is ● Eukaryotic transcription is catalyzed by three different
bound to the DNA template strand RNA polymerase:
■ Due to the weak binding of the Uracil Rich
Sequence to the DNA template, this will cause RNA POLYMERASE I
the dissociation of the RNA transcript from the ● “poly I”
template and this will cease transcription ● Responsible for making three rRNAs
OPERON RNA POLYMERASE II

● “poly II”
● Responsible for transcribing mRNA
RNA POLYMERASE III

● “poly III”
● Responsible for transcribing tRNA
● A transcription factor INITIATION

● Contains several segments of the gene
● It controls gene expression in bacteria or
microorganisms
● Parts of the Operon:
○ p - promoter for regulatory gene
■ Synthesizes the RNA polymerase
○ lac l - regulatory gene
■ Secrete or synthesize the repressor
○ p lac - promoter lac operon
○ O - operator
■ Regulates the gene expression
○ Genes that will synthesize the enzyme:
■ lac Z - synthesizes the beta-galactosidase
■ lac Y - synthesizes the beta-galactoside
permease
■ lac A - synthesizes beta-galactoside
transacetylase
NOTE: The aforementioned enzymes metabolize lactose.
When glucose is unavailable to the bacteria, they will
instead metabolize lactose to extract glucose.

AUF BSMT 3B & F 5
● Transcription Factor IID (TFIID) is composed of several ● The region of RNA that is downstreamed from the polyA
subunits including the TATA binding protein (TBP) signal sequence is cleaved by an exonuclease that
● TFIID will bind to the TATA box, thereby playing a role in degrades the transcript in the 5’ to 3’ direction
the recognition of core promoter ● Exonucleases then causes the RNA polymerase II to
● Then TFIID associates with TFIIB. TFIIB will then act as dissociate from the DNA
a bridge and promote the binding of poly II and TFIIF to
the core promoter
SUMMARY OF EUKARYOTIC TRANSCRIPTION
● TFIIE and TFIIH will bind to the RNA polymerase to
form a close complex or pre-initiation complex
● TFIIH has several subunits that plays a major role in the
formation of an open complex
○ One of which is a subunit that acts like the helicase
→ it will break open the hydrogen bond in between
the double stranded DNA
○ Another subunit hydrolyzes ATP and
phosphorylates a domain in the RNA polymerase
II, known as the Carboxyl Terminal Domain (CTD)
○ Phosphorylation releases the contact between the
RNA polymerase II and TFIIB, TFIIE, & TFIIH
● TFIIB, TFIIE, and TFIIH will proceed to the elongation
stage
● Transcription in the case of eukaryotes contains the
following:
ELONGATION ○ Promoter
○ TATA Box → repetitive sequence of
Thymine-Adenine
■ This will be the site for RNA synthesis
● There are proteins that will regulate the RNA synthesis:
○ First, the transcription factor will bind to the TATA
box because it must first proofread the DNA
sequence
○ Then, RNA polymerase can now bind and start to
synthesize the RNA
○ If the transcription factor is removed from the DNA
sequence, RNA synthesis will also stop
○ After RNA synthesis, modifications will occur
RNA PROCESSING
● In the elongation stage, eukaryotic mRNA are

elongated until RNA polymerase II reaches the
termination signal
TERMINATION
● After the RNA polymerase II has transcribed the polyA

signal sequence, the RNA is cleaved just downstream
of this sequence
● Proposed models of transcriptional termination of
eukaryotes:
ALLOSTERIC MODEL
● In this model, the RNA polymerase II become
destabilized after it has transcribed the polyA signal
sequence, eventually dissociated from the DNA
TORPEDO MODEL
● In this model, the RNA polymerase II is physically ● After the the preceding steps, modification in the RNA
removed from the DNA will occur:

AUF BSMT 3B & F 6
CAPPING AT THE 5’ END

● Recognition site for the ribosomes during the RNA
synthesis
● Protects the mRNA from degradation against enzymes
ADDING OF ADENINE AT THE 3’

● The addition of adenine will stabilize the mRNA
REMOVING AND RETAINING OF SEGMENTS

(MRNA)
● Introns are removed and exons are retained
● The enzymes that remove the segments (introns) in the
mRNA are called spliceosome
● Introns are removed because they are the non-coding
region of the RNA while the exons are the coding region
POST-TRANSCRIPTIONAL PROCESSING
BACTERIAL RNA
● When they are produced by transcription, they are ready
to be use and does not need to undergo any
significant alterations
EUKARYOTIC RNA
● All three types of RNA are processed extensively before
the transcripts are said to be mature, that is to say, rRNA
as part of the ribosomes, tRNA to actually interact with the
ribosomes during translation, and mRNA to be translated

AUF BSMT 3B & F 7
LECTURE | PROFESSOR: ISABELLE MAGLALANG
MODULE 6: GENE EXPRESSION: TRANSLATION OF THE GENETIC CODE
TRANSLATION
ELONGATION
● Peptide bonds are synthesized
● As the ribosome moves, the tRNA molecules
sequentially bind to the mRNA at the A site in the
ribosome, bringing with them the appropriate amino
acids
TERMINATION
● Recognizing of stop codons
● When the stop codon is reached, this will signal the
This stage is already the protein synthesis which occurs termination of translation
within the ribosome ● Disassembly occurs and the newly made polypeptide
will fall
GENETIC CODE
INITIATION
BACTERIA
● Initiation starts when the mRNA and the first tRNA

binds to the ribosomal subunits.
○ Ribosomal subunits - the large and small
subunits present in the diagram
● A specific tRNA will function as an initiator tRNA which
will recognize the start codon in mRNA.
● The genetic code is the information for linking amino ● In bacteria, the designated initiator tRNA is tRNA
acids into polypeptides under base sequence fmet
formylmethionine (tRNA )
● There are three base codons in mRNA ○ The initiator tRNA carries the formylmethionine,
● The genetic code is universal, meaning it is the same in context, the methionine has been covalently
for all organisms from bacteria to humans. modified.
○ The evidence is that we all came from a common ■ Formyl group (-CHO) is attached to the
ancestor nitrogen atom of the methionine
● Most important to remember are the start and stop fmet
codons. ● The mRNA, tRNA , and ribosomal subunits will be
○ AUG (Methionine) - start codon associated with each other to form an initiator complex.
○ UGA, UAA, UAG - stop codons ○ To fully form the initiator complex, the three
initiation factors should also be included which
are: IF1, IF2, and IF3.
STEPS IN TRANSLATION
● It involves three steps which are initiation, elongation,

and termination
INITIATION
● Start codon
● Wherein the ribosomal subunits, mRNA, and first tRNA
assemble to form a complex
○ When this initiation complex is formed, the
ribosomes lies along the mRNA in the 5’ to 3’
moving over the codons
PRADO | SANDOVAL
AUF BSMT 3F 1
● First, the IF1 and IF3 will bind to the 30S subunit and facilitates the binding of the mRNA to the 40S
wherein these IF will prevent the association of the 50S subunit.
subunit. ● After the initial binding of mRNA to the ribosome, the
● Then, the mRNA will bind to the 30S subunit which will next step is to locate the start codon or AUG that is
be facilitated by the Shine-Dalgarno sequence somewhere downstream from the 5’ cut structure.
○ Shine-Dalgamo sequence - within the bacterial When the start codon has been identified, the 60S
mRNA subunit assembles into the 40S subunit with the aid of
eIF5.
○ Researchers have found out that not all start
codons (AUG codons) near the 5’ end of mRNA
can function as start codons. There are some
cases where the ribosome will choose AUG
farther down the mRNA.
● Kozak’s rule
○ Hindi porket ikaw yung first AUG codon, ikaw na
ang pipiliin ng scanning ribosome. There are
several factors that need to be considered para
ikaws yung mapili. This applies to eukaryotes
ONLY. The sequences around the AUG codon
place an important role on whether siya ba yung
mapipili or not.
○ So para ikaw yung mapili, aside from the AUG
codon, a guanine at the positive 4 position and a
purine (preferably adenine) at the negative 3
position are the most important sites for
selection.
fmet
● tRNA binds to the mRNA wherein this step requires
ELONGATION
the IF2 which uses the guanosine triphosphate (GTP);
fmet
the tRNA will then bind to start codon. This tRNA
will then bind to the peptidyl site (or P-site of ribosome).
● IF1 will occupy a portion of an aminoacyl site which is
fmet
the A-site to prevent the binding of tRNA to the
A-site during initiation.
fmet
● When tRNA and mRNA are binded to the 30S
subunit, the IF1 and IF3 will be released. Meanwhile,
the IF2 will hydrolyze the GTP and then will be released
after. The 50S ribosomal subunit can now associate
with the 30S subunit
EUKARYOTES
● During the elongation stage, amino acids are added

one at a time in the polypeptide chain.
● Under normal cellular conditions:
○ BACTERIA – polypeptide chains can elongate
at a rate of 15-20 amino acids per seconds.
○ EUKARYOTES – polypeptide chains can
elongate at a rate of 2-6 amino acids per
seconds.
● For elongation to begin, a charged tRNA brings new
amino acids to the ribosome so it can be attached to the
● For eukaryotes, there are additional factors required for end of the growing polypeptide chain. The charged
the initiation process. The initiation factors are referred tRNA carrying a single amino acid will bind to A-site.
to as “eIF” or eukaryotic initiation factors. ● An elongation factor known as “EF-Tu” or elongation
● The initiator tRNA carries methionine instead of the factor thermo unstable (in bacteria) and “eEF1a” (in
formylmethionine used in bacterial initiation. Also, the eukaryotes) provides energy for the binding of tRNA to
eukaryotic mRNA do not have a Shine-Dalgarno (SD) the A-site.
sequence. ● So 16S rRNA will then ensure that there is proper
● eIF2 will bind directly to the tRNA to be able to recruit it recognition between the mRNA and correct tRNA.
to the 40S subunit. The mRNA will be recognized by the When 16S rRNA detects an incorrect binding of tRNA
ribosome through the eIF4 which is a multiprotein to the A-site, it will stop or prevent elongation until the
complex that recognizes the 7-methylguanosine cap
PRADO | SANDOVAL
AUF BSMT 3F 2
mispaired tRNA is released from the A-site–this process by the tRNA but instead by the proteins known
is known as the DECODING FUNCTION as RELEASE FACTORS (RF)
○ Decoding function is needed to maintain the high ○ BACTERIA - release factor 1 (RF1) recognizes
fidelity of the mRNA translation the UAA and UAG, while the RF2 recognizes the
UGA and UAA codons. Sometimes, third release
factor is also required
○ EUKARYOTES - a single RF, which is the eRF,
recognizes all of the three stop codons but there
is also eRF3 that is sometimes required in
termination
● Attached to the tRNA in the P site is the completed

polypeptide chain and in the A site is where the stop
codon is located.
PEPTIDYL TRANSFER REACTION

● This is the next step of elongation which is catalyzed by
a component known as the PEPTIDYL TRANSFERASE
● What happens here is that the polypeptide is removed
from the tRNA in the P site. From the P site, it will
transfer to the A site.
● While the transfer is happening, a formation of peptide
bonds occurs between the amino acid at the A site in
the polypeptide chain which lengthens the chain by one
amino acid
○ By sense, we only have three amino acids, but
when they are transferred from the P site going
to the A site, it will become from three to four.
● When the peptidyl transfer is complete, the ribosome
translocate to the next codon in the mRNA–this results
to the move of tRNAs at the P and A site to the E and P
site
○ After malipat ang amino acids mo, yung mga
tRNA from P and A site mamomove yan to the E
and P site. So mababalik rin lang yung mga amio
acids from the P site lilipat sila sa A site tapos
malilipat ulit sila ng P site. Then from P site
malilipat naman sa E site. (**medj magulo di ko
rin gets**)
○ E site stands for EXIT
● The next codon in the mRNA is now exposed in the
unoccupied A site.
○ Since A site is unoccupied, a charged tRNA can ● Either the RF1 or RF2 will bind to the stop codon at the
enter that A site A site then the RF3 will bind at a different location.
○ Suppose, the RF1 binds to the stop codon at the
TERMINATION A site and RF3 is already bound at another
location, then the bond between the polypeptide
and the tRNA is hydrolyzed. The polypeptide and
● This occurs when a stop codon is reached in the mRNA
the tRNA will then be released from the
○ In most species, the three stop codons are:
ribosome, then the ribosomal subunits along with
UAG, UGA, and UAA–these are not recognized
PRADO | SANDOVAL
AUF BSMT 3F 3
the mRNA and release factors will be

disassembled.
POSTTRANSLATIONAL MODIFICATIONS
● After the protein synthesis, the proteins must be folded

properly into three dimensional structure.
○ Sequence → structure → function
● The structure of the protein will serve as its function
○ Misfolded - ill effects
MISFOLDED PROTEINS ARE DESTROYED

● After translation, the proteins must be modified to make
them functional.
○ In translation, multiple copies of proteins are
made simultaneously.
● Ubiquitin will tag the misfolded proteins then the

Proteosome will dismantle the misfolded proteins.
PROTEIN FOLDING ○ It will then go back to peptides and amino acid,
● The modifications in proteins are called protein folding. and will be recycled once again to make proteins
● After synthesis, the proteins must be folded in a three
dimensional shape, and the enzymes and chaperone MISFOLDED PROTEINS
proteins will assist the proper folding of the proteins
because proteins can fold in more than one way.
○ If the proteins are not folded properly or correctly,
these proteins will be called MISFOLDED
PROTEINS–which can cause disease.
○ In order to prevent this, the misfolded proteins
are dismantled
LEVELS OF PROTEIN STRUCTURE
● Aberrant confirmation can be passed on propagating

like an infectious agent.
● When Alzheimer is familial, the onset of disease is
much earlier.
● Huntington disease has a late onset, it is an autosomal
dominant and lethal gene.
○ Lethal gene - when the lethal allele becomes
homozygous it will cause spontaneous abortion
PRADO | SANDOVAL
AUF BSMT 3F 4
PRIONS
● Prion is a protein folding disorder

○ Prp - normal prion
○ ScPrp - scrapie or mutant prion
● The mutant prion is acquired through the ingestion of
contaminated brain of cows or bovine
○ These scrapie/mutant prion will infect normal
prion and will deform these proteins to become
misfolded
● When prions are normal, there are no ill effects
○ But when these normal prions occurred in an
altered confirmation or was infected by a scrapie
prion, then this will cause a disease
● The infectious prions cause bovine spongiform

encephalopathy (BSE) for COWS
○ While for HUMANS, it is the variant
Creutzfeldt-Jakob disease (CJD)
● Mode of transmission for CJD is eating raw or
undercooked brains of cows
PRADO | SANDOVAL
AUF BSMT 3F 5
BSMT 3B | RAMOS, Maura Gale G.
TRANSLATION PROCESSES
PROKARYOTIC vs. EUKARYOTIC
Fast process [~20 residues Slower process [9 residues

per second] per second]
vastly smaller genome Discontinuous translation &
Synchronous and DNA as genetic transcription
continuous translation & material mRNA produced in the
transcription nucleus
mRNA produced in the
Same 20 essential Cap-independent & -
cytoplasm amino acids, 61 codons, dependent initiation
Cap-independent and 3 stop codons Performed by 80S
initiation Both involved in protein ribosomes
Performed by 70S synthesis. 9 initiation factors: elF 1, 2,
ribosomes Ribosome for protein 3, 4A, 4B, 4C, 4D, 5 and 6
Unstable mRNA Ribosomes: 40S & 60S =
Ribosomes: 30S & 50S =
synthesis 80S
70S Translation process: mRNA lifespan: few hours
mRNA lifespan: few INITIATION, to days
seconds to 2 mins. ELONGATION, Occurs in the G1 and G2
Occurs indefinitely TRANSLOCATION, phases of mitosis
Single release factor: eRF TERMINATION Release factors: RF1, RF2
3 initiation factors: IF1, IF2- 4 phases: gene regulation,
GTP, and IF3 elongation, termination,
and recycling
Stable mRNA
BYJU’S – The Learning App. (2023). Difference Between Prokaryotic And Eukaryotic Translation. https://byjus.com/biology/difference-between-prokaryotic-and-eukaryotic-translation/
M7 GENOME EVOLUTION
GENOME EVOLUTION wherein cytosine is replaced by guanine, for

• For the evolution of genomes, it is actually important which it will code to amino acid methionine,
for us to understand the processes that lead to the hence changing the amino acid sequence. We
variation among populations and specie. would then call that the missense mutation.
MUTATION
MUTATION
Change in DNA  The first step in process is the
sequence change in DNA sequence, referred
to as mutation.
Introduced  Mutation arises from a change in NONSENSE MUTATION:
through genetic sequence and this serve as • After the substitiution mutation, the resulting
replication a cause of diversity among codon is a stop codon. This would then cause the
error or DNA organisms so mutations may arise ribosome to stop translating the mRNA at the site
damage as a consequence of replication of mutation , and leading to the premature
error or DNA damage. termination of protein synthesis. With that we call
Mutation if  It is important to take note that if a nonsense mutations as “premature termination
protein coding mutation happened in the protein- codons”
region coding region, we can characterize
these mutations by the effect that
they have gene’s polypeptide gene
products
SYNONYMOUS VS. NONSYNONYMOUS MUTATIONS

• We can characterize such mutations as synonymous
or nonsynonymous
• Let us assume that a substitution mutation happens. In
FIXATION OF MUTATION
substitution mutation, a nucleotide is replaced by a
different nucleotide. • If mutation serves as the first stop of the process of
introducing variation of populations and species, the
second would be the fixation of this mutation over
SYNONYMOUS MUTATIONS
successive generations
• So, if a substation mutation happens, but there is no
• With the mutation becoming a feature of populations,
resulting change in the amino acid sequence, we
species or lineages, it is also important to know that the
call that a synonymous mutation.
mutations that are fixed are usually nucleotide
• We can understand it better by looking at the picture
substitutions
here:
o How do we know which mutations have a
higher probability of being fixed? The fate of
this mutations are dependent on natural
selection—meaning that it is dependent on
fitness.
▪ When we say fitness, we are talking
about the ability of organisms to
survive and reproduce in their
environment. If we are just talking
about natural selection, mutations
that improve the fitness of an
• As we can see here in the second codon, a organism would increase in
substitution mutation happened, which changed the frequency overtime, which would
nucleotide cytosine to adenine. However, the then result in fixation.
resulting codon would still code for the same amino • However, we have to consider that natural selection is
acid, which is isoleucine. So, we call that not the only factor that operates in this situation
synonymous mutation, because there is no resulting because we also have to consider neutral mutations.
change in the amino acid sequence.
NEUTRAL MUTATIONS
NONSYNONYMOUS MUTATIONS • These are mutations that do not affect the fitness of
• If there is a resulting change on the amino acid organisms (They neither harm, nor benefit an
sequence after substitution mutation, we call that as organism)
nonsynonymous mutation. • They are not affected by natural selection
• There are two type:
GENETIC DRIFT
MISSENSE MUTATION: • How can we determine which mutations are loss or
• The codon below codes for the amino acid, which mutations are fixed? Well, it is just dependent
isoleucine, a substitution mutation happens, on random chance, or in other words genetic drift
BSMT YR3 | 2ND SEM SCOOBYS 1

MODULE 7: GENOME EVOLUTION
• Genetic drift is the random changes in frequency in Figure 1: Gene A is duplicated then it acquires a new
a mutational variant in a population function and will become Gene C.
• Because the process of genetic drift is random, a
mutational variant can either be loss in the RETROPOSITION
population or a mutational variant can be fixed • A mechanism of gene duplication wherein a gene
wherein it will replace all the other variants transcript is used to generate retroposed gene
• But if we are just talking about genetic drift, we also copies (functional or non-functional)
have to note that genetic drift does not just affect o Non-functional: processed pseudogenes,
neutral mutations which is a DNA segments whose structure
• In genetic drift, most advantageous mutations are resembles a gene but isn’t capable of
eventually loss, whereas some weakly deleterious coding for a protein.
mutations may become fixed o These retroposed genes usually move to a
• Kumbaga, ang mga nakakabuti pang mutations sa new genomic environment where they
isang organism ang nawawala, at ang nagdudulot have to have regulatory elements or recruit
ng pinsala ang sya pang nananatili regulatory elements to become functional;
If not, they may become processed
EVOLUTIONARY RATE pseudogenes.
• When we compare genes or species, we typically use
the variation that come from fixed mutations WHOLE GENOME DUPLICATION (WGD)
• Because of that, we can also use them to estimate the • Offspring having twice the number of chromosomes
evolutionary rate which is the combination of the in each cell as their diploid parents. It can occur in
mutation rate and the fixation rate two ways:
• So if are talking about the neutral model, the o Two related species mated which led them
substitution rate is equal to the mutation rate, but to the formation of hybrid organism that
sometimes there is a disconnect between the two has the combined chromosome of both
values parents
• Minsan kapag nagcocompare tayo ng mga genes or o A single-celled embryo underwent
species, yung pagkakaiba ng dalawa is galing sa chromosome duplication wherein the
changes sa mutation rate at changes sa fixation rate duplicates stay in a single cell that
develops into a viable embryo
MECHANISMS OF GENOME EVOLUTION
• Transcription in the case of eukaryotes, there is a DUPLICATIONS ARE FORMED BY:
promoter and the TATA Box.
• Most genes are formed via: UNEQUAL CROSSING-OVER
o 80% by DNA-based duplication • A pair of homologous chromosomes come together
o 5 – 10% by de novo duplication/origination during meiosis in a way that they are not perfectly
o Approximately 10% by retroposition aligned (misaligned)
• Due to this, when there is genetic exchange
DEFINITION OF TERMS between the homologous; one chromosome would
EXONS  Coding sequences; contain have an extra segment of DNA (duplication) and
information to encode a protein the other chromosome would lose a DNA segment
(remain on a final RNA transcript) (deletion)
INTRONS  Intervening/non-coding sequences
(cut-out on a final RNA transcript)
REGULATORY  Contain information on the timing
SEQUENCES and intensity of gene expression
RETROPOSITION  Reverse-transcription of mRNAs
with the cDNAs being inserted into
the genome
NOTE: The generated retroposed gene copies do not have
introns and lack regulatory elements
1. DUPLICATION ROLLING-CIRCLE AMPLIFICATION

• Contribute most to the formation of new genes
• A process where a short DNA or RNA primer is
amplified to form a long single-stranded DNA or
DNA-BASED DUPLICATION
RNA using a circular DNA template on special DNA
• Involves the copying and pasting of DNA sequence or RNA polymerases
from one genomic region to another

2. DE NOVO ORGINATION • In other words, gene recombination involves the
combination of portions of existing coding sequences
to create a new gene
• It is best specified (exemplified?) by the illustration
which shows a chimeric gene called Jingwei, it is a
new gene that is identified through Drosophila yakuba
and Drosophila teisseri (fruit fly).
• Jingwei is formed due to the recombination of a
retroposed alcohol dehydrogenase derived
enzymatic domain, with the yellow emperor or YMP
hydrophobic domain of the Ymp gene
• On the other hand, new gene structure may also arise 5. NEW GENE REGULATORY SYSTEMS
from the De novo origination. • For new genes it is actually important for them to
• In De novo origination, genes emerge from a non- acquire a transcription regulatory system to ensure
functional DNA sequence that was previously not a temporal and spatial expression patterns.
gene. • In other words, these are important for temporal
• In the image, a mutation in a previously non-functional regulation, meaning, that a gene is only expressed at
sequence led to the formation of a new gene (purple a specific type and spatial regulation at a gene is
arrow) only expressed at a specific location.
3. HORIZONTAL GENE TRANSFER 6. TRANSPOSABLE ELEMENTS

• Transposable elements are elements that from one
place in a chromosome to another site, and it is
considered to contribute functional divergence in
duplicate genes.
• These transposable elements can actually mediate
gene recombination.
• Sa pamamagitan ng coding sequences mula sa isang
parte ng genome patungo sa ibang parte ng genome
at maari rin sila i-sama sa mga existing coding
sequences
MOLECULAR EVOLUTION OF REPETITIVE SEQUENCES

• To define repetitive sequences, these are
• New genes can also be generated from pre-existing
homologous DNA fragments that are present in
genes, in horizontal gene transfer, there is an
multiple copies on the genome, these are generated by
exchange of gene between genomes of distantly
a combination of molecular mechanisms like mutation,
related taxa.
unequal crossing-over and rolling circle
• In other words, pieces of DNA can be acquired from the
replication.
genome of one cell to another, even to a member of a
• In eukaryotic genomes, these repetitive elements are
different species.
considered to be components that evolved quite fast,
• In Prokaryotes, this actually serves as a major
because of this, they are used to differentiate species
mechanism to add new genes
that are related.
o Additional information, it is also important to
note the horizontal gene transfer is one of the
But if they are fast-evolving components, how can we determine
leading mechanisms for pathogenic bacteria
their evolution rate?
acquiring antibiotic resistance
• This is because horizontal gene transfer allows
• The evolution of these repetitive sequences are
bacteria to acquire antibiotic resistance genes from
correlated with their copy number, or the number of
other bacteria.
copies of a particular gene in an individual’s genome.
4. GENE RECOMBINATION
 Homogenous
LOW COPY NUMBER  Evolves slowly
 Heterogenous
HIGH COPY NUMBER  Evolves quickly
EVOLUTION OF THE PROKARYOTIC GENOME

• Prokaryotes live with genes that are much more
reduced in comparison to eukaryotes
FREE-LIVING PROKARYOTES
• Natural selection favors genome reduction
• New gene structures may also arise from gene • How did prokaryotes evolve strategies to cope with
recombination. a reduced gene set? There are two processes:
• Wherein existing exons are modified to produce new
chimeric genes, take note, chimeric. o Streamlining
o Muller Ratchet

THE STREAMLINING HYPOTHESIS
• Smaller genomes are favored for cellular
economization
o Because of this, genome reduction is
favored
• FREE LIVING PROKARYOTES
o Free living prokaryotes have a small
intergenic region, and they also have a
small cell size.
o Moreover, a low guanine and cytosine
content if these free-living prokaryotes live
in low nutrient environment.
▪ This is because of the energy cost
that is needed for nucleotide
synthesis and maintenance
▪ Mas gusto ng natural selection
pag mas mababa yung GC
content kase magastos sa energy
if mataas yung GC content
THE MULLER RATCHET

• Genome reduction happens through the
accumulation of slightly deleterious mutations
• Populations that undergo constant bottlenecks and
no recombination undergo genome reduction
through the accumulation of slightly deleterious
mutations
o This would then lead to the irreversible
deterioration of the genome
• NOTE: Muller Ratchet happens within ASEXUAL
population
o Dahil walang recombination na nangyayari
sakanila
ENDOSYMBIOTIC PROKARYOTES
• Function with a reduced gene set through:
1) Gene modifications of some genes coded in

reduced genome
o Allow the bacteria to cope when
essential genes are lost
2) Complementary genes in genomes of co-

symbiont
o Complementary genes of co-symbiont
may compensate to the ones lost by the
endosymbiont
3) Genes coded in genome of host

o Genes lost in the endosymbiont may be
compensated by the genes coded in the
genomes of the host

REFERENCES
❖ Alberts, B., Johnson, A., Lewis, J., Morgan, D., Raff, M.,
Roberts, K., & Walter, P. (2015). Molecular Biology of the
Cell (6th ed). Garland Science
❖ Iwasa, J., & Marshall, W. (2016). Karp’s Cell and
Molecular Biology (8th ed). John Wiley & Sons, Inc.
❖ Shen, C.H. (2019). Diagnostic Molecular Biology.
Academic Press.
BACO | CASTRO | DIMALANTA | PANTIG

AUF BSMT 3B & F 5
LECTURE MODULE 8: DNA MUTATIONS
MUTAGENESIS VS MUTATION MUTAGENS

• These are chemical or physical
Mutagenesis Mutation agents that are capable of inducing
• Change in DNA • Permanent and changes in the DNA.
• It is the change in the heritable change in • Pwedeng tobacco products,
DNA of an organism that genetic material which radiation, and wide variety of
result in a gene can result in an altered chemicals.
mutation protein function and
phenotypic changes MUTAGENS
CAUSES OF MUTATIONS
• Replication errors, mismatches

o Due to replication errors that
were able to evade the
proofreading function of the DNA
Polymerases
o Nagkakaroon ng mismatches
kasi they are position where the
• Mutagens are either:
nucleotide that is inserted into the
o Physical
daughter nucleotide does not
o Chemical
match
o Biological
o If this mismatch is retained then
Spontaneous this mutated version will be
PHYSICAL
Mutations carried over to the next round of
• Heat and radiation are the main causes of physical
replication
mutation
o So nagkakaron ng mismatched
and then this mismatch will • Heat
evade the proofreading function • Radiation (Ionizing and non-ionizing)
of the DNA polymerase, so
kapag naevade na yun, itong Ionizing radiation Non-ionizing radiation
mutated version mo will be • It is capable of inducing • It is NOT as strong as
carried over to the next round of changes or mutations in ionizing radiation to
replication our germ cells. directly affect the
• These are gene mutations that you • It acts upon gonads or structure/ atom or cause
are born with. germ cell, causing the DNA damage.
• This can be because of mutagens genetic material to be • However, it does cause
that may acted with the parent altered which can vibration in the atoms
DNA that cause structural changes eventually lead to that cause them to heat
that inter affect the base pair genetically induced up.
capability of the altered diseases. o Heat can also cause
nucleotide. o However, genetically mutations.
Induced induced diseases do
• These is the gene mutation that
Mutations not entirely arise
happens after birth that can be
caused by either: from radiation
o Environmental factors exposure but can
o Lifestyle also be due to
• Both can cause mutations in your environmental factors.
gene, AFTER BIRTH.
Module 8: DNA Mutations 1

CHEMICAL POSSIBLE EFFECTS OF POINT MUTATION
Cigarette smoke Causes dozens of mutagenic Silent • No alteration in amino acid

chemicals sequence of polypeptide even
though the nucleotide sequence has
Nitrate and From processed food (like fast changed.
nitrite foods) • Hindi nagmanifest yung disease or
preservatives changes, silent lang siya
Barbecueing Creates mutagenic chemicals in • In genetic code, several codons can
the food code for proline (parang ganto yung
nangyayare)
BIOLOGICAL Missense • Changes are visible
• Infectious agents such as viruses or bacteria • Merong changes sa amino acid
• Example: Human Papilloma Virus (HPV) and • Ex: sickle cell anemia
Helicobacter pylori Nonsense • Involves a change between a normal
o H. pylori is first bacterium classified as carcinogen. codon to stop codon
• This terminated the translation of a
TYPES OF MUTATIONS polypeptide, earlier than expected.
Point • Commonly occurred type SICKLE CELL ANEMIA
mutation
• When one or more base pairs are
Deletions lost from the DNA resulting in a
frameshift
Insertion • Addition of a number of nucleotides
POINT MUTATION
• It is a genetic disorder that results because of a

difference in a single nucleotide in the DNA of the
carrier; as compared to the DNA if the non-carrier.
• This difference occurs in the change of the genes that
code for the one of the sub-units of hemoglobin, the
protein carries oxygen throughout the body.
• In the template strand, there is adenine instead of
thymine.
o So in term, the adenine stand will code for a uracil so
• Aka “Base substitution” it can match the sequence of the template strand.
• Change in a SINGLE base pair within the DNA o So our codon will now change from glutamic acid
o Ex: GAG → CTC (GAG) to valine (GUG) para nga ma-match iyong
• Under this mutation, we have the two types: Transition template strand, iyong mRNA mo, it will change from
and Transversion adenine to uracil.
TRANSITION TRANSVERSION Template

GGA–CAC–CTC
strand
• One purine or • Purine is substituted for
CCU–GAG–GAG
pyrimidine is replaced a pyrimidine or vice
mRNA to
by another versa
CCU–GUG–GAG
• Pyrimidine to Pyrimidine • If the original is
ang changes pyrimidine, it’ll change
• Different yung hydrophobic side chain ng valine sa
• Purine to Purine ang to purine
glutamic acid, so, the mutations will result in a
changes • Or if the original is
conformational change.
purine, it’ll change to
pyrimidine • This will then cause the hemoglobin to aggregate in low
oxygen concentration, forming hemoglobin fibers. This

will cause the normal blood cells to be distorted in a rigid DELETIONS
sickle shape that can clog small blood vessels.
Normal Red Blood Sickled Red Blood Cells

Cells
• Shorter sequences in deletions which can result in a

truncated protein product
o Truncated – means shorter
• This type of mutation is the cause of a large number of
genetic diseases like the Cri-du-chat syndrome or “cat
(Sickle Cell Anemia)
cry”
o Kasi yung newborn na affected with this, yung tunog
FRAME SHIFT MUTATIONS ng iyak niya is comparable dun sa cats
• Both deletions and insertions can be classified under
frameshift mutations because the entire reading frame
of the genetic code gets shifted. DNA REPAIR SYSTEM
• Sa frameshift mutation, almost all result into a non-
functional protein. 1 Direct Repair
2 Base Excision Repair and Nucleotide Excision
INSERTION DELETION Repair
The addition of one or The removal of one or 3 Mismatch Repair
more base pairs in the more base pairs in the 4 Homologous Recombination Repair
sequence. sequence 5 Nonhomologous End Joining
INSERTION 1. DIRECT REPAIR

• An enzyme recognizes an incorrect alteration in the
DNA structure and directly converts it back
• So, yung damaged nucleotide mo, directly narerepair
yan, kailangan mo lang ng particular enzyme for that
repair to happen.
2. BASE EXCISION REPAIR AND NUCLEOTIDE

EXCISION REPAIR
• Yung damaged base/nucleotide is recognized then
removed, from the DNA. So, a segment from the DNA
is excised (damaged part). Then yung complementary
• For example, that is your mutation site, kunwari ang DNA strand is used as a template to synthesize a
normal base pairs mo dito is 20 base pairs, so dahil nga normal DNA.
insertion yan, dito sa part na to (mutation site), mag-
aadd ng another base pairs (adenine and thymine), • Initiated by an enzyme known as
which will result in a 21 base pairs. DNA N-Glycosylase
o So, ang mangyayari nyan is mag-iiba na yung o This type of enzyme can
reading frame mo kasi nga diba by 3s ang bilang sa recognize an abnormal base and
codons, instead na magcode yan for proline, cleave the bond between it and
magcocode yan ng different amino acid mo Base excision the sugar in the DNA backbone.
o Magcchange yung manifestation ng disease or repair This creates an apurinic or
magkakaroon ng phenotypic changes apyrimidinic site.
o You do not immediately assume na magmamanifest • Repairs corrects DNA damage
yung disease from oxidation, deamination and
alkylation

• It takes place in nuclei and 4. HOMOLOGOUS RECOMBINATION REPAIR
mitochondria • This occurs during Double Strand Breaks (DSB).
• Protects us against cancer, aging, o Or when the DNA damage causes a gap in the
and neurodegeneration synthesis during replication.
Nucleotide • Several nucleotides are removed • This is usually used to repair those DNA double strand
excision from the DNA, so the intact strand breaks or DSB.
repair is used as a template for the • Para maintindihan natin ng mas maayos ito yung
synthesis of the normal nangyayari:
complementary strand.
• It is the main pathway used by
mammals to remove the DNA
regions such as those formed by
UV light, environmental mutagens
and some cancer
chemotherapeutic adapts from the
DNA.
• Diseases or deficiencies here are
often associated with the skin.
XENODERMA PIGMENTOSUM
• One example
is the
Xenoderma
pigmentosum,
in which the
skin has
increased
sensitivity with
sunlight.
• Near
impossible to
repair UV induced lesions.
• This disease involves a defect in
genes that are involved with the
Nucleotide Excision Repair
(NER) 1 • First, ang mangyayari is the double strand break
• Affected individuals has: is recognized
1. Increased sensitivity to
sunlight because of an
inability to repair UV
induced DNA lesions.
2. Pigmentation abnormalities
3. Many premalignant lesions
4. High predisposition to skin
2 • Then, digestion happens
cancer.
3. MISMATCH REPAIR
• Enzyme recognizes an incorrect alteration in the DNA
structure and directly converts it.
• It is similar to excision repair, except the DNA defect in
the base pair mismatch is not an abnormal nucleotide.
• What happens here is that the mismatch is recognized
right away which occurred during the replication. 3 • Instead na ganito yan hindi kasi pwede na iwan
• Once it recognizes the mismatch, the repair system sya na ififill-in lang yung sa gap nito di ba kasi
excises that part of the daughter polynucleotide and fills kailangan na mag-iba ng base pairs mo.
in the gap.

4 • Mas prone sa errors kapag iyan lang ang irerepair
mong part. Saan papasok yung unbroken strand
mo dyan sa kaliit na space dyan di ba?
5 • So kapag nagkaroon na ng digestion sa DNA

break site mo, it will be followed by the exchange 5. NONHOMOLOGOUS END JOINING
of DNA strands between the broken and • Two broken ends are simple pieced back together.
unbroken chromatidsome. Kaya ka nagdigest,
papasok nyan itong unbroken mo sa part nato. 1 • So, double strand break is recognized again.
• Then ito naman sa papasok sa part nato:
• So, magkakaroon ng crisscrossed dyan. Kapag

naresolve na yan, yung broken strands mo are
will join in a way that produces separate
chromomatids. So, from crisscrossed, unbroken
strands are used as templates and then
mareresolve na.
• So, ang advantage nito is because your sister

chromatid mo ay genetically identical, this
recombinantion repair can be error free
mechanism. Kasi identical naman yung mga yan.

• So, meron kayong End binding proteins that
will recognize sa break side mo HELA CELLS
3
• HeLa Cells are used by researchers around the world

• So, in order for the strands na hindi maghiwalay as the human cell line.
or to prevent two ends from drifting apart. • The human cell line is obtained from a 51-year-old
Magkakaroon ka ng proteins mo. woman named Henrietta Lack, thus the name HeLa
• Yung end binding proteins mo, cell.
magrerecognize pa yan ng iba pang proteins • This woman died from cervical cancer in 1951 (the
para hindi magdrift apart yung dalawang strand picture above is the obtained biopsy sample from
mo nay an. Henrietta)
• So, this will create a bridge. • The cell line is used to study the effect of toxins,
4 drugs, hormones, and viruses on the growth of
cancer cells without experimenting on humans.
• It is also used to test radiation and poison on the
human genome to learn how viruses work.
• It also played a crucial role on the development of polio
vaccine.
• After that, a small amount of deletion may occur o This is due to scientists needs one model or one cell
during this process. line so the effects can be replicable or the experiment
• Magkakaroon ng deletions dun sa nakabilog na can be replicated.
red o Thus, in order to verify studies, need the same yung
• Finally, the gaps are filled in via DNA gamit niyo.
polymerases and then, the DNA ends are ligated
together
• Disadvantage: It can result in a small deletion in TWO-HITS HYPOTHESIS
the region that has been repaired • Introduced by Alfred Knudson in 1971
o When there is deletion, there will be truncated • Unifying model for understanding cancer
product so the sequence will be shorter o Carrier of the susceptible gene
o Induced mutations
Non-Homologous Homologous ▪ This hypothesis provided a unifying model for
• Can only occur during • Can occur at any stage understanding cancer that occurs in individuals
specific stage of the of the cell cycle who carry a susceptible gene and cancer that
cell cycle particularly, S- • Advantageous develop because of induced mutations.
stage o Can commit less error • In Knudson’s study, he had 48 patients with
• Joined directly but because of its retinoblastoma. He obtained the age, when they were
before this happened, identical strands diagnosed, sex, family history, and if the tumor occurred
there are already ▪ That is why in one eye or in both eyes. Then, he estimated the
deletion happened in crisscross number of tumors present in each eye. At the time of his
that part. happened study, researchers believe that retinoblastoma could be
caused by either somatic or germline mutation.
• Based from his data approximately 40% of the US cases
CANCER: GENETIC DISORDER of Retinoblastoma was caused by a germ line mutation.

• However, he was wondering since some children with • Transformed cells are stimulated to the environment
affected parents didn’t have the disease, but instead within and outside the cells which influences cancer
those unaffected children, they already had a child, then development.
the manifestation of the disease was seen in those
children. 3. PROGRESSION
• He found out that an individual can inherit the mutation • Cells or tumor cells compete with one another to survive
but have the disease. which leads to more mutations that can make the cell
• There is a saying in genetics that even though it is not more aggressive.
yet proven, “every 3rd generation the disease is o Yung tumor mo will increase in size, then mutation
manifested,” this what happen here, the parent is further occurs in the cell which leads to
affected, then the diseases are not manifested in the heterogeneity.
child but it possesses the genes. This is might be ▪ Heterogeneity: refers to multiple genetic variants
because the gene is recessive and in the 3rd generation
(the children future child) the disease is manifested. But GENE MUTATIONS
again, this is not yet proven. • Mutations at birth + acquired mutations = cancer
o Mutations present at birth and mutations acquired
throughout life lead to cancer
CARCINOGENESIS o E.g. You inherited a genetic mutation that
• This is a process by which normal or healthy cells predisposes you to cancer, you still need other gene
transform into cancer cells. mutations for the cancer to manifest.
• May result from any combination of chemical, physical, • Inherited gene mutation could make you more likely
biological, and/or genetic insults to the cell. than other people to develop cancer when expose to
• It is divided into three stages: cancer-causing substances
o Initiation o E.g. despite having *Aa gene of a disease, there
o Promotion should be other factors/insults muna for the
o Progression disease to manifest
o *A – dominant gene; a – recessive gene
1. INITIATION
ADDITIONAL NOTE:
Mutations cannot be entirely good or bad. It is essential
to the continuity of life and evolution of organisms
• Genetic alterations occur.

• So, the cell is exposed sa carcinogen mo. Then, this will
predispose the susceptible normal cell to malign
evolution.
• Fast and irreversible. And it is transmitted to the
daughter cell.
• We have two kinds of initiators.
o Direct Acting Carcinogen
o Indirect Acting Carcinogen.
Direct Acting Indirect Acting

Carcinogens Carcinogens
• These do not require • These require
metabolic activation in metabolic activation on
order to become a the other hand in order
carcinogen. to become a
carcinogen.
2. PROMOTION

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MOLECULAR BIOLOGY AND DIAGNOSTICS

LECTURE | PROFESSOR: MA. CLARIZ ISABELLE MAGLALANG

MODULE 1: INTRODUCTION TO MOLECULAR BIOLOGY AND DIAGNOSTICS

● In his experiment, he injected different types of bacterial

○ Carbohydrates ● They were able to label the DNA using the T2

D. RNA IS THE GENETIC MATERIAL FOR VIRUSES

Nucleoside WITHOUT phosphate group

Nucleotide WITH phosphate group

● Monocyclic base with six (6) membered ring

1 Two long polynucleotide chains are coiled around a

2 The two DNA strands are antiparallel, that is, their 5’

3 The base of both chains lie perpendicular to the axis,

DNA DNA DOUBLE HELIX

5 Each complete turn of the helix is 34˚ angle long

6 The double helix has a diameter of 20˚ angle

7 The amount of adenine (A) residues is proportional

8 The sum of the purines is equal to the sum of

9 The percentage of (G+C) is not necessarily equal

JAMES WATSON ● Involves two polynucleotide strands that are coiled

JAMES WATSON AND FRANCIS CRICK HYDROGEN BONDING INTERACTIONS

Image of Watson and Crick elucidating the 3D structure of

● It is the formation of hydrogen bonds between

BASE STACKING INTERACTIONS REFERENCES

● Gives the staircase appearance of the DNA

ALTERNATIVE FORMS OF DNA

● These are similar to the normal DNA we know, but

A-DNA Observed when DNA is dehydrated or under

It is right-handed and turns clockwise

B-DNA Exist under very high humidity environment

It is right-handed and turns clockwise

Z-DNA Formed under high salt or in the presence of

Longer and narrower than B-DNA

It is left-handed and turns counterclockwise

Essential amino acids are standard amino acids needed

Disulfide bonds Strongest Form covalent bond to stabilize

Electrostatic “Salt Amino acids with charged side

transfer RNA (tRNA) - supplies amino acids to the ribosome to be

As the hydrogen bonds between the base pairs are

Helicase Primase DNA Polymerase Ligase

Helicase Primase DNApolymerase Ligase

strands form new strands

NUCLEIC ACID STRUCTURE AND FUNCTION | Lead Editor: Bob Moss

Translation: DNA to mRNA to Protein

https://www.nature.com/scitable/topicpage/translation-dna-to-mrna-to-protein-393/ 2/21/23, 22:46

https://www.nature.com/scitable/topicpage/translation-dna-to-mrna-to-protein-393/ 2/21/23, 22:46

Where Translation Occurs

The Beginning of mRNA Is Not Translated

https://www.nature.com/scitable/topicpage/translation-dna-to-mrna-to-protein-393/ 2/21/23, 22:46

Translation Begins After the Assembly of a Complex Structure

https://www.nature.com/scitable/topicpage/translation-dna-to-mrna-to-protein-393/ 2/21/23, 22:46

https://www.nature.com/scitable/topicpage/translation-dna-to-mrna-to-protein-393/ 2/21/23, 22:46

Table 1: N-Terminal Sequences of Proteins

N-Terminal Percent of Percent of

MK** 10.59% 2.50%

MS* 9.41% 11.67%

MT* 7.65% 6.67%

* Methionine was removed in all of these proteins

** Methionine was not removed from any of these proteins

Figure 5: The large ribosomal subunit binds to the small