Module 5: DNA replication, Protein synthesis, and Gene Regulation

THE UNTOLD STORY OF THE LEGENDARY CHINESE RECIPE

In the old Library, there is a legendary chinese recipe that is written in Mandarin.

Many people always read this legendary book, and always secure a copy.

Bringing out of books is not allowed so people were trained to photocopy the recipe.

After having the copy of the book, people get out of the library because library is not meant for cooking, so
people go to their houses to cook this legendary recipe.

But wait,

The recipe is written in Mandarin.

But people used to translate the language using their dictionary.

Once they have translated the entire recipe, they start now to cook this in their kitchen.

During cooking, the ingredients were added, taste is being modified before it is served.

After all, the dish now is ready to serve!

Have a nice meal.

***
Direction: At the end of this module, I would like you to relate this story to the main topic of this module.

Module objectives:
This module will give you the details of the concepts on Central Dogma of Molecular Biology, DNA
replication and protein synthesis. Specifically, this module aims to:
(1) discuss the Central Dogma of Molecular Biology;
(2) elaborate the concept of Central Dogma by discussing the entire processes of DNA replication
and protein synthesis;
(3) identify the enzymes that catalyze throughout the reactions of the abovementioned cellular
processes; and,
(4) using the genetic markers, identify the causes, signs and symptoms, and possible treatment for the
following genetic disorders and diseases.
INTRODUCTION

(a) (b) (c)

_____________________________________________________________________________
(a) King Penguin. Retrieved from: https://seaworld.org/animals/all-about/penguins/reproduction/
(b) Mitosis. Retrieved from: https://pixels.com/featured/2-mitosis-artwork-sciepro.html
(c) DNA Replication. Retrieved from: https://www.mechanobio.info/genome-regulation/how-is-dna-replicated/

One of the characteristics of living things is to reproduce another organism. But this process can be
seen in different biological levels of organization. In species level, reproduction can be in sexual or asexual
reproduction. In the given the given illustration, penguins reproduce by combining the gametes of the two
parent penguins. In cellular level, cells undergo the process of mitosis by using the genetic materials of the
parent cells to produce identical daughter cells. In the molecular level, parent strand of the DNA is
duplicated through the process of DNA replication.

Genes are made up of DNA molecules that determine the characteristics of organisms. This
statement provides structural and functional definitions of genes. Structural definition characterizes its
chemical composition, the DNA, and functional definition describes how genes determine the possible
phenotypes or characteristics of the organisms once these molecules are expressed.

TASK 1: WATCH AND LEARN!

Direction: Watch the following videos for Monday discussions in Cell and Molecular Biology. Focus on the
entire process by listing down the important enzymes that are utilized in the process and the
products that are produced per stages of the process. Make a comprehensive summary per
video.

DNA Replication

https://youtube.com/watch?v=IjVLhoyfGAM&feature=share https://www.youtube.com/watch?v=Qqe4thU-os8
 DNA Repair Mechanism Protein Synthesis

https://www.youtube.com/watch?v=vP8-5Bhd2ag https://www.youtube.com/watch?v=oefAI2x2CQM

Make a comprehensive summary of these videos.

https://www.youtube.com/watch?v=h_1QLdtF8d0

I. INTRODUCTION TO CENTRAL DOGMA OF MOLECULAR BIOLOGY

The central dogma of molecular biology describes the two-step
process, transcription and translation, by which the information in
genes flows into proteins: DNA → RNA → protein.
• Transcription is the synthesis of an RNA copy of a segment
of DNA. RNA is synthesized by the enzyme RNA
polymerase.

• Translation is the process of converting the message of the

RNA into sequences of amino acids, the building block of
proteins.

In a prokaryotic cell,
transcription and
translation are coupled; that is, translation begins while the mRNA
is still being synthesized. In a eukaryotic cell, transcription occurs
in the nucleus, and translation occurs in the cytoplasm. Because
there is no nucleus to separate the processes of transcription and
translation, when bacterial genes are transcribed, their transcripts
can immediately be translated.

Transcription and translation in prokaryotic cell

 In eukaryotic cell, transcription and translation are spatially and
temporally separated; that is, transcription occurs in the nucleus to
produce a pre-mRNA molecule. The pre-mRNA is typically
processed to produce the mature mRNA, which exits the nucleus
and is translated in the cytoplasm.

Different Genes for Different RNAs

There are 4 types of RNA, each encoded by its own type of gene.
The genomic DNA contains all the information for the structure and
function of an organism. In any cell, only some of the genes are
expressed, that is, transcribed into RNA.

Transcription and translation in eukaryotic cell

There are 4 types of RNA, each encoded by its own type of gene:
• mRNA - Messenger RNA: Encodes amino acid sequence
of a polypeptide.
• tRNA - Transfer RNA: Brings amino acids to ribosomes
during translation.
• rRNA - Ribosomal RNA: With ribosomal proteins,
makes up the ribosomes, the organelles that translate the
mRNA.
• snRNA - Small nuclear RNA: With proteins, forms
complexes that are used in RNA processing in
eukaryotes. (Not found in prokaryotes.)

Basic Structure of a Protein-Coding Gene

A protein-coding gene consists of a promoter followed by the
coding sequence for the protein and then a terminator.

• The promoter is a base-pair sequence that specifies where transcription begins.

• The coding sequence is a base-pair sequence that includes coding information for the polypeptide
chain specified by the gene.
• The terminator is a sequence that specifies the end of the mRNA transcript.

II. PROTEIN SYNTHESIS

The Transcription Process

RNA synthesis involves separation of the DNA
strands and synthesis of an RNA molecule in the
5' to 3' direction by RNA polymerase, using one
of the DNA strands as a template. In
complementary base pairing, A, T, G, and C on
the template DNA strand specify U, A, C, and
G, respectively, on the RNA strand being
synthesized. Transcription begins at the promoter, proceeds through the coding region, and ends at the
terminator.

mRNA in Prokaryotes
The sequence of a prokaryotic
protein-coding gene is collinear
with the translated mRNA; that is,
the transcript of the gene is the
molecule that is translated into the
polypeptide.

mRNA in Eukaryotes
The sequence of a eukaryotic
protein-coding gene is typically not
collinear with the translated
mRNA; that is, the transcript of the
gene is a molecule that must be
processed to remove extra
sequences (introns) before it is
translated into the polypeptide.

Most eukaryotic protein-coding

genes contain segments called introns, which break up the amino acid coding sequence into segments called
exons. The transcript of these genes is the pre-mRNA (precursor-mRNA).

The pre-mRNA is processed in the nucleus to remove the introns and splice the exons together into a
translatable mRNA. That mRNA exits the nucleus and is translated in the cytoplasm.

Pre-mRNA Processing (Splicing)

Eukaryotic pre-mRNAs typically include
introns. Introns are removed by RNA
processing in which the intron is looped
out and cut away from the exons by
snRNPs, and the exons are spliced
together to produce the translatable
mRNA.

The steps of pre-mRNA splicing (intron

removal) are as follows:
• The intron loops out as snRNPs
(small nuclear ribonucleoprotein
particles, complexes of snRNAs
and proteins) bind to form the
spliceosome.
• The intron is excised, and the
exons are then spliced together.
• The resulting mature mRNA may
then exit the nucleus and be translated in the cytoplasm.
Generally, protein synthesis follows these steps:

TASK: To further understand this cellular process, it is recommended for you to watch the videos from
youtube.com. These videos are downloaded already inside the course pack.
1. Protein Synthesis! (Mr. W's Rock Music Video)
2. Protein Synthesis and the Lean and Mean Ribosomes

Processes in Protein Synthesis Function of the enzyme(s)

 Transcription------- RNA polymerase (to produce mRNA)
 Initiation---------endonuclease; helicase - unwind the double helix structure of
DNA
 Elongation --------- RNA polymerase - catalyzes the elongation or addition of
nucleotide until it reaches the termination
 Termination -------- RNA polymerase stage.
 Translation - Amino-acyl transferase (to translate mRNA sequence to amino acids/protein)
 Initiation - signal by formyl-methionine signals translation
 Elongation ---- Amino-acyl transferase - catalyzes the addition of amino acids
 Termination -----Amino-acyl transferase forming polypeptide chains using the
(signal by stop codon) pairing of codons until it reaches the stop
codon.
 The Universal Genetic Code

In translation, the three codons of mRNA code for specific amino acid. This table will
help you determine what amino acid code by the mRNA. Remember, mRNA contains the
message of the DNA, the anticodon of tRNA just pair with mRNA. For example, proline is
coded by the codons, CCU, CCC, CCA, CCG. This triplet code only codes for a specific amino
acid while one amino acid can be coded by different triplet codes except for the start codon,
methionine.

You can also use this chart to determine the specific amino acid but be mindful in
reading. It should be from the center of the chart going to the corner which the amino acids lie.
EXERCISE NO.1
Using the genetic code table above, determine the amino acid the code for the following triplet codes

1. CAU _________________ 6. UGC __________________

2. ACU _________________ 7. AGC __________________
3. AAA _________________ 8. UCG __________________
4. ACG _________________ 9. GGA __________________
5. GUG _________________ 10. AUG __________________

EXERCISE NO.2
Based on the videos and previous exercise, complete the information for the steps in protein synthesis

#1 DNA template 3’ – TAC – GTC – TAG – GGA – ATT – 5’

mRNA ______________________________________
 tRNA ______________________________________

Amino acid sequence ______________________________________

#2
DNA template ______________________________________

mRNA 5’ – AUG – AAG – CCU – AAU – UGA – 3’

tRNA _______________________________________

Amino acid sequence _______________________________________

#3
DNA template _______________________________________

mRNA _______________________________________

tRNA (UAC) (UAU) (AGC) (AAA) (ATC)

Amino acid sequence _______________________________________

III. DNA Replication

DNA replication is a semi-conservation cellular process that duplicates the copies of the genetic materials
of the organisms. This cellular process is responsible for the perpetuation of cells since this is involved in
the Synthesis phase once the cell undergoes cellular division.

TASK 2: To further understand this cellular process, it is recommended for you to watch these video from
youtube.com. These videos are downloaded already inside the course pack.
• DNA replication process in 3D Animation
• What happens when your DNA is damaged?

Questions:
1. Why is DNA replication described as semi-conservative process?
 2. What are the functions of the following enzymes and molecules in the DNA replication process?
2.1. Helicase 2.6. primers
2.2. Single stranded binding proteins 2.7. primase
2.3. DNA Gyrase 2.8. Okazaki fragment
2.4. DNA polymerase II 2.9. DNA ligase
2.5. DNA polymerase I
3. What is continuous and discontinuous synthesis? Why these processes take place?
4. What would be the consequence(s) once the DNA replication fails? Does it have repair mechanism?

NOTE: The video will help you to answer the questions above.

IV. GENETIC MARKERS for GENETIC DISORDERS and GENETIC DISEASES

• Genetic disorders are the innate genetic health problems associated with the mutation and/or change
on the expressions of the genes.

• Genetic diseases are the acquired genetic health problems that are triggered by the viruses, bacteria,
fungi and other organisms that cause to change the mutation and/or expression of the genes.

TASK 3: Complete the table given below by identifying the causes (genetic markers), signs and symptoms
of the following genetic disorders and diseases, and the ways of treatments.

Genetic disorder of diseases Causes (genetic Signs and Ways of

marker/s) Symptoms treatments
1. Sickle-cell anemia

2. Hemophilia

3. Lactose intolerance
4. Breast Cancer

5. Patient with cri-du-chat

syndrome

6. Duchenne muscle
dystrophy

7. Diabetes mellitus type 2

WRITTEN ASSESSMENT
Direction: Read the question carefully and encircle the letter of the best answer.

1. The main product of transcription is _______________.

a. rRNA c. mRNA
b. tRNA d. amino acids

2. Which of the following sequences is correct for central dogma of molecular biology?
a. DNA → tRNA → mRNA → protein
b. DNA → mRNA → tRNA → protein
c. DNA → protein → mRNA → tRNA
d. DNA → tRNA → protein → mRNA

3. What will happen if transcription stage is omitted in gene expression?

a. DNA will mutate
b. The amino acid sequence is more stabilized.
c. RNA will still be produced.
d. No polypeptide will be produced.

4. ATG is the start codon of gene expression, this codon codes for what amino acid?
a. Arginine c. Lysine
b. Glycine d. Methionine

5. The three stop codons in protein synthesis are _____________.

a. UAG, UGA, UAA c. UUA, UGA, UUA
b. UGG, UUA, UAG d. UAG, UAA, UUG

6. The DNA sequence, 5’- TAC-AAT-TCG-ACT-3’ would have an mRNA sequence of

_______________.
a. 5’- AUG-AGC-UUA-UAG-3’ c. 5’-AUG-UUA-AGC-UGA-3’
b. 5’-ATG-AGC-TTA-TAG-3’ d. 5’-ATG-TTA-AGC-TGA-3’

7. Based on question number 6, the complimentary DNA sequence is _____________.

a. 3’- AUG-AGC-UUA-UAG-5’ c. 3’-AUG-UUA-AGC-UGA-5’
b. 3’-ATG-AGC-TTA-TAG-5’ d. 3’-ATG-TTA-AGC-TGA-5’

8. What is the enzyme that catalyzes addition of nucleotide to the newly synthesize strand of DNA?
a. DNA polymerase I c. DNA polymerase II
b. RNA polymerase d. DNA Gyrase
 9. What is the enzyme that catalyzes initiation, elongation and termination in transcription stage of
protein synthesis?
a. DNA polymerase I c. DNA polymerase II
b. RNA polymerase d. DNA Gyrase

10. What is the enzyme that countercheck the correct sequence and repair the DNA if in case
addition of nucleotide is incorrect?
a. DNA polymerase I c. DNA polymerase II
b. RNA polymerase d. DNA Gyrase

PERFORMANCE BASED ASSESSMENT

TASK 5
1. Create a model or instructional material that simulates the process of:
a. DNA replication
b. Protein synthesis
2. Your model can be a combination of the two processes or you may create separate models.

Samples of protein synthesis model

DNA Replication Model

REFERENCES
Retrieved from:
(a) King Penguin. Retrieved from: https://seaworld.org/animals/all-about/penguins/reproduction/
(b) Mitosis. Retrieved from: https://pixels.com/featured/2-mitosis-artwork-sciepro.html
(c) DNA Replication. Retrieved from: https://www.mechanobio.info/genome-regulation/how-is-dna-
replicated/
(d) Central Dogma of Molecular Biology.
http://www.phschool.com/science/biology_place/biocoach/transcription/overview.html
(e) Genetic Code. https://byjus.com/biology/genetic-code/
(f) Genetic Code Chart. https://jgi.doe.gov/proving-codon-genetic-code-flexibility/
(g) Duchenne Muscle dystrophy https://www.semanticscholar.org/paper/Valley-sign-in-duchenne-muscular-
dystrophy%3A-in-with-Pradhan/e88611035c90b385c0c91497c3e4d56d8c85076f
(h) Diabetes Mellitus II https://www.atulpeters.com/blog/diabetes-mellitus-type-ii-permanent-solution/

MODEL RUBRIC
Exemplary Exceeds Standard Adequately Meets Below Standard Student
4 3 Standard 1 Score
2
▪ High quality ▪ Student ▪ Understanding at ▪ Shows little or
CONTENT

student developed rote or no

explanations explanations definitional level understanding
▪ evidence of ▪ can apply ▪ follows ▪ fails to follow
meaningful concepts when directions directions
learning problem solving _______
▪ applies concepts in ordinary
in new situations situations

▪ Accurate, ▪ Contributes to ▪ Minimal ▪ Does not

VISUALIZATION (REPRESENTATION)

precise, & valid understanding of contribution to contribute to

model concepts/ understanding of understanding of
▪ model is process concepts/ real world
adaptable to ▪ appropriate processes concepts/
changes in display of data ▪ follows ▪ processes
variables (novel ▪ appropriate use directions ▪ incomplete
situations) of model ▪ appropriate use ▪ does not follow
components of design directions
▪ valid components &
mathematical software
model

_______