STM127 Lesson-1
STM127 Lesson-1
STM127 Lesson-1
GENETICS
CONTEXT
Learning Competency
At the end of the lesson, the learners can:
a. diagram the steps in DNA replication and protein synthesis;
b. illustrate the molecular structure of DNA, RNA, and proteins.
EXPERIENCE
Prelection: The Words
Directions: Select any three words from the list provided below and provide definitions for
them based on your comprehension
1. ___________________ - ___________________________________________________
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2. ___________________ - ___________________________________________________
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3. ___________________ - ___________________________________________________
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Processing Question:
How are these terms related in the context of Genetics?
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Concept Notes
Genetics has enabled people to understand the basis for the traits acquired from the
previous generation. Genetics explains a lot of things. Studying genetics can help us know
details about our own health; thus, we can make healthy choices. Also, studying genetics
can give us vast knowledge about how to improve the productivity of certain domesticated
plant species that are economically important to us.
Genetics plays a big role in our society. By having an in-depth understanding of genetics,
we can really learn a lot of things that will help us survive. The central dogma of molecular
biology is the basic underlying principle in the field of genetics. This explains that DNA
codes for RNA, which codes for proteins
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COMPONENTS OF THE CENTRAL DOGMA OF MOLECULAR BIOLOGY
Deoxyribonucleic Acid or DNA is the genetic material passed on from parents to offspring. It
contains the instructions necessary for the survival of every organism. Most of the cells in the
body of an organism contain DNA, but its locations vary.
In prokaryotes such as bacteria, DNA is located in the nucleoid region in the cytoplasm. In
eukaryotes, DNA is often located in the membrane-bound nucleus, but some may be found in
the mitochondria.
The DNA model, proposed by biologists Francis Crick and James Watson in 1953, is a double
helix structure that twists spirally, similar to a twisted ladder or a spiral staircase. The two
helices may coil either clockwise or counter clockwise. Its backbone or building block, called
the nucleotide, is composed of a phosphate group, a sugar, and nitrogenous bases.
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Components of Nucleotides
a. Phosphate Group
The phosphate group in the DNA is composed of a phosphorus atom surrounded by four
oxygen atoms. By itself, the nucleotide may have three phosphates. However, when joined
to the growing strand of DNA, two of its phosphates are lost, and the remaining one
attaches to another nucleotide’s sugar.
The sugar group in DNA is called deoxyribose. The prefix deoxy- in “deoxyribose” means
that ribose has lost an oxygen atom. The five-carbon structure of ribose in the DNA
molecule is numbered, based on its carbon atom. The carbon atom on the right side is
assigned as number 1, and the numbering sequence runs clockwise.
In the figure shown below, the absence of an oxygen atom on the second carbon in the
deoxyribose sugar helps distinguish DNA from RNA. This also makes DNA a relatively
stable molecule, as it is less likely to get involved in chemical reactions.
The last carbon in the ribose sugar is numbered as 5’ (read as “five-prime”). Notice that
there is a apostrophe or stroke after the number. The small mark in the numbering
distinguishes it from any of the numbers given to atoms in the other rings. Its importance
will be discussed in detail as we learn about DNA replication and translation.
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c. Nitrogenous Bases
The nitrogenous bases in the nucleotide can be classified according to the number of rings in
their structure. Purines, which are adenine and guanine, have a double-ringed structure, and
the pyrimidines, which are cytosine, thymine and uracil, contain only one ring in their
structure. Uracil is usually found in RNA and serves as the counterpart of thymine in DNA.
The nitrogenous bases undergo complementary base pairing, wherein each pair should
contain a purine and pyrimidine. Each nucleotide is paired together by forming hydrogen
bonds. In DNA, adenine (A) is paired with thymine (T), and guanine (G) is paired with
cytosine (C). Uracil (U) replaces thymine in RNA.
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2. RIBONUCLEIC ACID (RNA)
Imagine that you need to get specific information from a manual, but you cannot bring the
manual home. Thus, you photocopy the pages in the manual that have the information you
need. This scenario can be linked to one involving DNA and RNA. At the cellular level,
your DNA serves as the “manual,” and the RNA serves as its “photocopy.” When the cell
needs to get information that codes for a specific protein, RNA will copy that information,
which is stored in DNA. This helps the cell get the instructions needed to produce the
protein, while keeping the DNA information intact.
Years ago, people thought that RNA helps only in creating proteins. However, it was
recently discovered that the roles of RNA are much broader that what scientists thought
they were. Recently, biologists learned that RNA can also act as enzymes, which speed up
chemical reactions in the body. RNA also helps in regulating various cell processes,
ranging from cell division, differentiation, and growth, to cell aging and death. It was also
discovered that certain RNA defects can result in human diseases. How DNA and RNA
works will be discussed in detail as we tackles protein synthesis.
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3. PROTEINS
Proteins are the final products in the central dogma of molecular biology. They are called the
building blocks of life because they have diverse functions in the body. First, proteins serve as
structural support. A very good example of this kind of protein is collagen. Collagen supports
your body and connects your muscles and bones together. Collagen also makes up your hair
and skin. Second, proteins aid in transporting molecules around your body. An example of this
kind of protein is hemoglobin, which is a protein found in red blood cells. Hemoglobin carries
oxygen from your lungs to all the parts of your body. Proteins also act as enzymes. Your
salivary glands, stomach, and intestines create different kinds of enzymes that break down the
food you eat into nutrients that can be absorbed by your cells. On the other hand, an enzyme-
specifying gene can help produce a surface antigen in the red blood cell, which determines
your blood type. Last, proteins act as a passageway of molecules and substances into and out
of the cell.
Figure 1.11 Proteins that aids in Transport Figure 1.12 Proteins that act as a passageway
Source: askhematologist.com Source: 2012books.lardbucket.org
Proteins are composed of polymers of numerous amino acids known as polypeptides. The
three-dimensional structure of a protein not only defines its size and shape, but also its
function. The folding in a protein structure allows for interactions between amino acids that
are distant to each other. Scientists have identified 20 amino acids so far. These amino acids
can potentially be configured into more unique information-carrying structures. The properties
of the proteins are determined by the order of the amino acids in the polypeptide.
There is a system by which the particular order of nitrogenous bases in DNA and RNA can be
translated into specific amino acids in a polypeptide. The language of instruction in the
mRNA is called the genetic code.
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How can a code with just four letters carry instructions for 20 different
amino acids?
The secret is that the genetic code is read using a combination of only three letters at a time.
Thus each word of the coded message is three bases long. The three-letter combination in the
mRNA is known as a codon. Table below shows the amino acids formed by 64 possible
codons of the genetic code.
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Observe that some of the amino acids can be specified by more than one codon. However,
few codons can specify only one amino acid. Also, note that three codons are referred to as
STOP codons – UAG, UGA, and UAA.
As mentioned earlier, DNA codes for proteins. This process involves transcription and
translation. DNA transcription is first process wherein the important information in the DNA
strand is copied into the mRNA. The next step is translation, wherein the information sent
by the mRNA is analyzed with the help of ribosomes. The ribosomes translate the mRNA
code into the proper protein format.
What is the importance of DNA replication and protein synthesis in the human body?
DNA replication is important for the replacement of damaged or dead cells as well as for the
proper formation of gametes needed for fertility. In fact, the importance of DNA replication is
difficult to overstate. Errors in DNA replication can lead to diseases, including cancer, an
important topic in the area of replication biology.
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DNA REPLICATION
DNA replication is the process by which DNA makes a copy of itself during cell division.
DNA replication occurs in all living organisms acting as the most essential part of biological
inheritance.
Both of them can serve as a template for the new strand. DNA replication in prokaryotes is
easy because it usually begins at a single point in the chromosome. However, eukaryotes have
a great challenge because DNA replication usually occurs at hundreds of sites in the cell.
Different enzymes are important for carrying out DNA replication. These enzymes unzip DNA
molecules by breaking down the hydrogen bonds between base pairs. As the strands of DNA
molecules unwind or separate, the original strands serve as a template for the attachment of
complementary strand with the bases.
For example, a strand with the bases ACGTTA would produce a complementary strand with
the bases TGCAAT. The resulting complementary strand of DNA molecules is identical to the
original strand. Thus, each DNA molecule undergoing replication produces one original strand
and one new strand.
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3 Major Steps of DNA Replication
1. INITIATION
This is the first major step in DNA replication. In this process, an enzyme called helicase
unwinds and separates the DNA into two single strands. This happens when the hydrogen
bonds between the nitrogenous bases are broken. Usually, the starting point, or the origin of
replication, happens in adenine and thymine because only two hydrogen bonds are in
between them. Guanine and cytosine have three hydrogen bonds in between them. The
structure formed from this process is called the replication fork.
Next, the RNA primase binds the RNA nucleotides to the initiation point of the 3’–5’ parent
strand. The RNA nucleotides act as the primer, or the starting point for DNA synthesis. Once
the primer nucleotides are attached to the template DNA, the RNA primase exits in
preparation for elongation.
2. ELONGATION
Elongation occurs when an enzyme called DNA polymerase adds DNA nucleotides to the 3’
end of the added RNA nucleotide. The addition of DNA nucleotide is specified by the
nitrogenous bases in the template strand, wherein only those complementary to the template
nucleotides are added to the new strand.
Leading Strand Elongation: The leading strand is the DNA strand that is synthesized in the
same direction as the movement of the replication fork. This fortunate alignment allows for
relatively straightforward and continuous synthesis. DNA polymerase catalyzes the addition
of complementary nucleotides to the 3' end of the RNA primer or the growing DNA strand.
Crucially, DNA polymerase moves in the 3' to 5' direction along the template strand, which
happens to align with the 5' to 3' direction of DNA synthesis. This fortunate coincidence
enables the leading strand to be elongated continuously, as the polymerase can efficiently add
new nucleotides in the proper order. Because of this continuous synthesis, there is no need for
DNA ligase to join separate fragments. As a result, the leading strand remains as a single,
unbroken piece of newly synthesized DNA.
Lagging Strand Elongation: In contrast, the lagging strand presents a more complex
challenge during DNA replication. It is synthesized in the opposite direction to the movement
of the replication fork due to the antiparallel nature of DNA. While DNA polymerase also
synthesizes the lagging strand in the 5' to 3' direction, consistent with the synthesis of both
strands, it encounters a problem because the replication fork is moving in the opposite
direction. This incompatibility results in a unique mode of synthesis known as discontinuous
synthesis. The lagging strand is synthesized in fragments known as Okazaki fragments. This
process begins with the action of primase, an enzyme that lays down short RNA primers at
regular intervals along the lagging strand template. These primers serve as starting points for
DNA synthesis by DNA polymerase. DNA polymerase then extends the primers, generating
short segments of DNA known as Okazaki fragments. Each Okazaki fragment typically spans
from a few hundred to a few thousand nucleotides.
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Figure 1.18 Comparison of the Leading and Lagging Strand
Source: teachmephysiology.com
3. TERMINATION
This is the last step in DNA replication. In this process, the DNA polymerase halts when it
reaches a section of the DNA template that has already been replicated. However, this event
does not end the entire DNA replication process. In the lagging strand, there are gaps where
the primers were present. These primers have been removed because an enzyme called
exonuclease strips the RNA primers away. These RNA primers need to be replaced with DNA.
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As soon as the RNA primers are removed, a free-floating DNA polymerase will attach to the
3’ end of the DNA fragment. Finally, an enzyme called ligase seals up the sequence into two
continuous double strands, resulting in two DNA molecules. The DNA replication process is
usually described as semiconservative because half of the DNA is composed of the old
template strand and the other half is composed of the newly synthesized strand.
In DNA replication, all processes should be controlled. The “proofreading” function of the
DNA polymerase helps prevent mistakes in the replication process. As the DNA polymerase
moves along a single strand of DNA building the complementary strands, the base pairing is
checked. How are errors in base pairing detected? If a wrong nitrogenous base has been
inserted into the DNA strand, it causes an unstable bond that the DNA polymerase can easily
recognize. Once detected, the wrong nitrogenous base is soon replaced by the DNA
polymerase itself.
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Table 1.1 Enzymes and Proteins Involved in Replication
Enzymes and Proteins Specific Function
DNA Pol I Exonuclease activity and removes RNA primer and replaces
with newly synthesized DNA
DNA Ligase Seals the gaps between the Okazaki fragments to create one
continuous DNA strand
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What happens when a mismatch does occur?
An answer to this question emerged when researchers found pol III (DNA polymerase III)
mutants in E. coli with error rates that were 100 times greater than normal. The defect was
localized to a particular portion of the enzyme, called the € (epsilon) subunit. Further
analysis showed that this subunit acts as an exonuclease – meaning an enzyme that peels
nucleotides off of DNA.
The Pol III exonuclease activity turned out to be directional. The enzyme removes
nucleotides only in the 3’-5’ direction. These results led to the conclusion that Pol III can
proofread. In other words, if the wrong base is added during DNA synthesis, the enzyme
pauses, removes the mismatched base, and then proceeds with synthesis.
This proofreading activity reduces Pol II’s error rate to about 1 x 10-7 (one mistake per 10
million bases).
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Mutation is a much broader phenomenon than single base changes in a DNA sequence. A
mutation is defined as any change in an organism’s genome. Mutations result from the
insertion or deletion of DNA sequences, changes in chromosome number or content due to
error in meiosis and chromosome breaks that leads to segment of the genome being flipped –
a phenomenon known as a chromosome inversion. Several types of mutation occur
independently of the replication process.
The mutational mechanisms reviewed here are important. At the level of individuals, they
can cause disease and death. Currently, the mutations attracting the genes responsible for
repairing damaged DNA.
What will happen if there is no “proofreading” that takes place during DNA replication?
What might be the negative effects of this scenario?---------------
DNA replication is a highly accurate process, but mistakes can occasionally occur, such as a
DNA polymerase inserting a wrong base. Uncorrected mistakes may sometimes lead to
serious consequences, such as cancer. Repair mechanisms correct the mistakes. In rare
cases, mistakes that are not corrected may lead to mutations; in other cases, repair enzymes
are themselves mutated or defective.
Imagine making a random change in a complicated machine such as a car engine. The
chance that the random change would improve the functioning of the car is very small. The
change is far more likely to result in a car that does not run well or perhaps does not run at
all. By the same thought, any random change in a gene's DNA is likely to result in a protein
that does not function normally or may not function at all. Such mutations are likely to be
harmful. Harmful mutations may cause genetic disorders or cancer.
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DNA TRANSCRIPTION
The process by which RNA is synthesized from DNA is called transcription. This process is
the first stage in the central dogma of molecular biology. Transcription happens when a DNA
is the portion is copied to form its complementary mRNA sequence. For prokaryotes,
transcription occurs in the cytoplasm. But we’ll simply divide it into three steps for easier
understanding.
2. ELONGATION
As mentioned in the previous process, only one of the unmounted DNA strands acts as a
template for mRNA synthesis. Elongation happens when different nucleotides from the
cytoplasm are added to the growing RNA chain. Similar to DNA replication, RNA is also
synthesized in the 5’–3’ direction.
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3. TERMINATION
Termination happens when RNA polymerase reaches the terminator site. The terminator site
contains a specific sequence of nucleotides that signals the end of transcription. When this
happens, transcription stops along with the release of the RNA polymerase and the
transcribed mRNA strand. The terminator consists of a series of adjacent adenines which is
preceded by a nucleotide palindrome that stops the RNA polymerase from transcribing any
further. Then, the DNA double helix reforms.
mRNA MODIFICATION
Before translating mRNA to proteins, it undergoes modification by several different
processes, such as RNA splicing, 5’ end capping, and adding a poly-A tail.
1. RNA splicing
RNA molecules produced in transcription require a bit of editing before getting translated.
Even a few rRNA molecules, which are produced from larger RNA molecules, are also cut
and trimmed to their final sizes. To modify RNAs into usable forms, large pieces known as
introns or intervening sequences are cut out while they are still in the nucleus. The
remaining portions called the exons or expressed sequences are then spliced back together to
form the final mRNA. Although the reason for this process cannot be explained completely,
scientists have suggested that introns and exons may have played a vital role in evolution.
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Figure 1.24 RNA Splicing
Source: phschool.com
2. 5’ end capping
Aside from RNA splicing, 5’ end capping is another way of modifying the produced mRNA
into its functional form. This process protects the mRNA from exonuclease activity that might
degrade the mRNA. It also regulates nuclear transport and promotes the translation and the
excision of the introns.
3. Poly-A tail
Poly-A tail is the shortcut for polyadenylation, which allows the addition of multiple
adenosine monophosphates at the end of the mRNA molecule. This means that a stretch of
adenine bases is added to the tail end of the mRNA. This process produces mature mRNA that
is ready for translation. The addition of adenine bases at the end of mRNA also protects it
from enzymatic degradation in the cytoplasm and aids in the termination process.
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Table 1.2 Enzymes involved in Transcription
Enzymes Functions
Helicase Unwind and start strand seoaration
RNA polymerase Brings complementary base – matching nucleotides
Ligase Corrections and gap corrections
Promoter sequence On mRNA – signals ‘’ start’’ for transcribing DNA sequence into
RNA sequence
TRANSLATION
The sequence of nucleotide bases created in mRNA after transcription serves as a code for the
order of amino acids to be joined together. There should be mechanism that translates this
code. Translation happens when the message carried by mRNA is decoded into a protein
subunit.
INITIATION
This is where the mRNA that was transcribed inside the nucleus is released into the
cytoplasm. It starts when the ribosomal subunits, especially the small unit, binds to the 5’
strand of the mRNA until it encounters the start codon (AUG). Note that translation also
works in the 5’–3’ direction. The presence of the start codon initiates translation. Each tRNA
molecule found freely in the cytoplasm has an anticodon, which is composed of a set of
three nitrogenous bases in the tRNA molecule that is complementary to one of the mRNA
codons. The ribosome portions the start codon AUG at the P site to attract its anticodon
which is part of the initiator tRNA that binds methionine. The next tRNA would arrive at the
P site of the ribosome.
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ELONGATION
As each of the codon moves through the ribosomes, the proper amino acid is brought into the
ribosome and is attached to the growing polypeptide chain. Elongation is simply the formation
of the growing polypeptide chain by bringing in the proper tRNA to translate the mRNA into a
protein.
TERMINATION
Continuous attachment of tRNA to the mRNA allows the polypeptide chain to elongate until
in encounters a STOP codon (UAA, UAG, or UGA), which terminates and completes the
process of translation. There are no tRNA molecules with anticodons for STOP codons.
Instead, the stop codon would signify protein release factors that would release the
polypeptide from the ribosome. Then, the ribosome splits into its subunits, which can later be
reassembled for another round of protein synthesis.
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Table 1.3 Enzymes involved in Translation
Enzymes Functions
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Guided/Independent Practice
1. Color the complimentary DNA strand using DNA base pairing rules.
2. Color the correct mRNA bases by transcribing the correct DNA code.
3. Translate the mRNA codons and find the correct amino acid using the Codon Table.
4. Write in the amino acid and the correct anti-codon the tRNA molecule.
A.
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Guided/Independent Practice
B.
A C A T T C
A G A
A G A
A C U
C.
A G T
T A T
A A G U A G
U U U
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5’
D.
3’
G G T G T A
G T A G G A
C A A
5’
E.
3’
C G A G A A G C T
A T G C C A
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REFLECTION-ACTION
Writing to Learn Worksheet 1
2. What new information did you learn from the topic? Include new terms and their meaning.
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Processing Questions:
DNA mutation can cause genetic disease that could affect the person’s overall phenotypic
function that could lead to a lifetime of impairment due to the disease. It is important to
realize, that these random aberration in the genes were never the choice of the people to have
them and has occurred to them by chance due to their genetic ancestry. What do you think
would happen if culturally we allow first cousins to marry?
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EVALUATION
A. Summative Exam: 1st Summative Exam (50 points)
The goal is to make a thorough and useful case study that shows
Goal how genetic disorders affect people and their families and helps
people understand how complicated genetic inheritance can be.
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CASE STUDY RUBRIC
Distinguished Proficient Apprentice Novice Limited
Criteria
(5) (4) (3) (2) (1)
Exceptional Poorly
introduction that Adequate constructed
Strong introduction
provides a clear and introduction that introduction
Introduction
information that
provides a solid information that may not information
demonstrates a deep
understanding of the covers the basics sufficiently that does not
understanding of the
subject matter, but may lack support the effectively
subject matter,
including relevant depth or evaluation and support the
including relevant
details and concepts. organization. proposed project.
historical context and
solutions.
key concepts.
Comprehensive
evaluation that
critically analyzes the
Evaluation of the Case
Adequate
case, including the Solid evaluation of Basic
evaluation of the Superficial
identification of key the case that evaluation that
case that evaluation that
issues, causes, and identifies key issues identifies
identifies some lacks depth and
implications. and their causes, limited issues
key issues and fails to identify
Demonstrates a providing a clear or causes
causes but may key issues or
thorough analysis of the without in-
lack depth or causes.
understanding of situation. depth analysis.
clarity in analysis.
relevant factors and
their
interrelationships.
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Distinguished Proficient Apprentice Novice
Criteria
(5) (4) (3) (2)
Well-considered and
Basic proposed
Proposed Solution/
creative proposed
Thoughtful proposed Adequate proposed solutions or
solutions or changes
Changes
that somewhat
is directly aligned that effectively recommendation that
summarizes the
with the proposed summarizes the project's summarizes key points
project's points
(x2)
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