3

STUDY GUIDE FOR MODULE NO. ___

Chapter 3: Chemical Basis of Heredity

MODULE OVERVIEW

Protein structure Protein sources

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The genetic substance of all living creatures, from viruses to man is a complex chemical
compound- the nucleic acid DNA (deoxyribonucleic acid) the instructions in DNA are transmitted
by messenger RNA (ribonucleic acid). Chromosomes are made from DNA. Genes are short
sections of DNA. DNA carries the genetic code that determines the characteristic of a living thing.
A gene is a short section of DNA. Each gene code for a specific protein by specifying the order in
which amino acids must be joined together. The cell’s nucleus contains chromosomes made from
long DNA molecules.

MODULE LEARNING OBJECTIVES

1. Review the history of DNA structure and function

2. Determine DNA structure and function:
3. Describe the process DNA replication
4. Compare and contrast DNA and RNA
5. Describe the role of DNA in directing RNA synthesis
6. Describe Role of DNA in directing protein synthesis
7. Explain the process of protein synthesis

LEARNING CONTENTS I & II. Background, DNA & RNA

I. Background review: Important terms

Proteins. These are large, organic complex molecules that play many critical roles in the body.
They do most of the work in cells and are required for the structure, function, and regulation of
the body's tissues and organs. Proteins are made up of hundreds or thousands of smaller units
called amino acids, which are attached to one another in long chains. They invariably have the
general formula RCH(NH2)COOH, where C is carbon, H is hydrogen, N is nitrogen, O is oxygen,
and R is a group, varying in composition and structure, called a side chain.

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Amino Acids. Chemically, protein is composed of amino acids, which are organic compounds
made of carbon, hydrogen, nitrogen, oxygen or sulfur. Amino acids are the building blocks of
proteins, and proteins are the building blocks of muscle mass
Amino acids are classified into three groups: (https://rb.gy/5zegdm)
a) Essential amino acids. These cannot be made by the body. As a result, they must come
from food. The 11 essential amino acids are: histidine, isoleucine, leucine, lysine,
methionine, phenylalanine, threonine, tryptophan, and valine.

Amino Acid Food Sources

1 Histidine Soy protein, eggs, parmesan, sesame, peanuts
2 Isoleucine Eggs, soy protein and tofu, whitefish, pork, parmesan
3 Leucine Eggs, soy protein, whitefish, parmesan, sesame
4 Lysine Eggs, soy protein, whitefish, parmesan, smelts
5 Methionine Eggs, soy protein, whitefish, parmesan, smelts, sesame
6 Cysteine Eggs, soy protein, parmesan, smelts, sesame, mustard seeds
7 Phenylalanine Eggs, soy protein, whitefish, peanuts, sesame
8 Tyrosine Eggs, soy protein, whitefish, sesame, parmesan
9 Threonine Eggs, soy protein, parmesan, smelts, sesame
10 Tryptophan Eggs, soy protein, parmesan, winged beans, chia seeds
11 Valine Eggs, soy protein, parmesan, beef, sesame

b) Nonessential amino acids. Nonessential means that our bodies produce an amino acid,
even if we do not get it from the food we eat. Nonessential amino acids include: alanine,
arginine, asparagine, aspartic acid, cysteine, glutamic acid, glutamine, glycine, proline,
serine, and tyrosine.
c) Conditional amino acids. Conditional amino acids are usually not essential, except in
times of illness and stress. Conditional amino acids include: arginine, cysteine,
glutamine, tyrosine, glycine, ornithine, proline, and serine. When the body experiences
 periods of extreme trauma or stress from thermal injury, sepsis, surgery, or wounds,
nonessential amino acids become conditionally essential, or conditionally
indispensable. The physiological demands of recovery may result in the need for these
nonessential amino acids to be greater than the body’s ability to produce them. As a
result of these demands, the body’s supply of nonessential amino acids must be
provided by the diet.

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We do not need to eat essential and nonessential amino acids at every meal, but getting
a balance of them over the whole day is important. A diet based on a single plant item will not be
adequate, but we no longer worry about pairing proteins (such as beans with rice) at a single
meal. Instead we look at the adequacy of the diet overall throughout the day.
There are 20 amino acids that make up proteins and all have the same basic structure,
differing only in the R-group or side chain they have. The simplest, and smallest, amino acid is
glycine for which the R-group is a hydrogen (H). They can be subdivided according to their
properties, dictated by the functional groups they possess. Broadly they are divided by charge,
hydrophobicity and polarity. These properties influence the way they interact with surrounding
amino acids in polypeptides and proteins, and consequently impact protein 3D structure and
properties (https://rb.gy/he3fbv).
Below is the list for the 20 amino acids:
Alanine Isoleucine Tyrosine
Arginine Leucine Valine
Asparagine Lysine
Aspartic acid Methionine
Cysteine Phenylalanine
Glutamic acid Proline
Glutamine Serine
Glycine Threonine
Histidine Tryptophan
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Nucleotide. A nucleotide is the basic building block of nucleic acids. RNA and DNA are polymers
made of long chains of nucleotides. A nucleotide consists of a sugar molecule (either ribose in RNA
or deoxyribose in DNA) attached to a phosphate group and a nitrogen-containing base. The bases
used in DNA are adenine (A), cytosine (C), guanine (G), and thymine (T). In RNA, the base uracil (U)
takes the place of thymine.
C, T, and U are called pyrimidines and each has a single nitrogen-containing ring. A and G
are called purines and each has two nitrogen-containing rings (https://rb.gy/rwx4kn).

Nucleic Acids. These are naturally occurring chemical compound that is capable of being broken
down to yield phosphoric acid, sugars, and a mixture of organic bases (purines and pyrimidines).
Nucleic acids are the main information-carrying molecules of the cell, and, by directing the process of
protein synthesis, they determine the inherited characteristics of every living thing. The two main
classes of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA is the
master blueprint for life and constitutes the genetic material in all free-living organisms and most
viruses. RNA is the genetic material of certain viruses, but it is also found in all living cells, where it
plays an important role in certain processes such as the making of proteins.
Video: https://rb.gy/sn2xej

II. TYPES OF NUCLEIC ACIDS:

A. DNA:
DNA is the chemical name for the molecule that carries genetic instructions in all living things.
The DNA molecule consists of two strands that wind around one another to form a shape known as
a double helix. Each strand has a backbone made of alternating sugar (deoxyribose) and phosphate
groups. The sugar and phosphates are nucleotide strands that form the long sides. The nitrogen
bases are the rungs. Every rung is actually two types of nitrogen bases that pair together to form a
complete rung and hold the long strands of nucleotides together.
Attached to each sugar is one of four bases known as nucleotides-adenine (A), cytosine (C),
guanine (G), and thymine (T). The two strands are held together by hydrogen bonds between the
bases; adenine bonds with thymine, and cytosine bonds with guanine. The sequence of the bases
along the backbones serves as instructions for assembling protein and RNA molecules
(https://rb.gy/7i4whc)
Human DNA is unique in that it is made up of nearly 3 billion base pairs, and about 99 percent
of them are the same in every human. However, it is the sequence of these bases that determines
what information is available to both build and maintain any organism.
The twisting of the strands allows DNA to be more compact. In order to fit within the nucleus,
DNA is packed into tightly coiled structures called chromatin. Chromatin condenses to form
chromosomes during cell division. Prior to DNA replication, the chromatin loosens giving cell
replication machinery access to the DNA strands (https://rb.gy/4k5zq1).
Think of DNA like individual letters of the alphabet – letters combine with one another in a
specific order and form to make up words, sentences, and stories. The same idea is true for DNA –
how the nitrogen bases are ordered in DNA sequences forms the genes, which tell our cells how to
make proteins. Ribonucleic acid (RNA), another type of nucleic acid, is formed during the process of
transcription (when DNA is replicated). RNA’s function is to translate genetic information from DNA to
proteins as it is read by a ribosome. (https://rb.gy/96vsjg)

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How Does DNA Work? (https://rb.gy/96vsjg)

DNA is essentially a recipe for any living organism. It contains vital information that’s
passed down from one generation to the next. DNA molecules within the nucleus of a cell wind
tightly to form chromosomes, which help keep DNA secure and in place and store important
information in the form of genes to determine an organism’s genetic information.
DNA works by copying itself into that single-stranded molecule called RNA. If DNA is
the blueprint, you can think of RNA as the translator of instructions written in the blueprint.
During this process, DNA unwinds itself so it can be replicated. RNA is similar to DNA, but it
does contain some significant molecular differences that set it apart. RNA acts as a
messenger, carrying vital genetic information in a cell from DNA through ribosomes to create
proteins, which then form all living things.

B. RNA (https://rb.gy/uafqyj)

Ribonucleic acid (RNA) is an important biological macromolecule that is present in all

biological cells. It is principally involved in the synthesis of proteins, carrying the messenger
instructions from DNA, which itself contains the genetic instructions required for the development and
maintenance of life. In some viruses, RNA, rather than DNA, carries genetic information.
Ribonucleic acid (RNA) is formed during the process of transcription (when DNA is replicated).
RNA’s function is to translate genetic information from DNA to proteins as it is read by a ribosome

Types of RNA and their roles (https://rb.gy/4k5zq1)

There are several types of ribonucleic acid, or RNA, but most RNA falls into one of three
categories.
1. mRNA or Messenger RNA
mRNA transcribes the genetic code from DNA into a form that can be read and used
to make proteins. mRNA carries genetic information from the nucleus to the cytoplasm of a
cell.

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2. rRNA or Ribosomal RNA

rRNA is located in the cytoplasm of a cell, where ribosomes are found. rRNA directs
the translation of mRNA into proteins.

3. tRNA or Transfer RNA

Like rRNA, tRNA is located in the cellular cytoplasm and is involved in protein
synthesis. Transfer RNA brings or transfers amino acids to the ribosome that corresponds to
each three-nucleotide codon of rRNA. The amino acids then can be joined together and
processed to make polypeptides and proteins.

The type of RNA dictates the function that this molecule will have within the cell. Aside from
the coding region of messenger RNA (mRNA) molecules that will be translated into proteins, other
cellular RNA elements are involved in different processes, which include transcriptional and post-
transcriptional regulation of genetic material, temperature and ligand sensing, translation control and
RNA turnover.

Table Comparison of DNA and RNA

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While both DNA and RNA are used to store genetic information, there are clear differences between them.
This table summarizes the key points:
Main Differences Between DNA and RNA
Comparison DNA RNA
Name Deoxyribonucleic Acid Ribonucleic Acid
Function Long-term storage of genetic information; Used to transfer the genetic code from the
transmission of genetic information to make nucleus to the ribosomes to make proteins. RNA
other cells and new organisms. is used to transmit genetic information in some
organisms and may have been the molecule
used to store genetic blueprints in primitive
organisms.
Structural B-form double helix. DNA is a double- A-form helix. RNA usually is a single-strand helix
Features stranded molecule consisting of a long consisting of shorter chains of nucleotides.
chain of nucleotides.
Composition of deoxyribose sugar ribose sugar
Bases and phosphate backbone phosphate backbone
Sugars adenine, guanine, cytosine, thymine bases adenine, guanine, cytosine, uracil bases
Propagation DNA is self-replicating. RNA is synthesized from DNA on an as-needed
basis.
Base Pairing AT (adenine-thymine) AU (adenine-uracil)
GC (guanine-cytosine) GC (guanine-cytosine)
Reactivity The C-H bonds in DNA make it fairly stable, The O-H bond in the ribose of RNA makes the
plus the body destroys enzymes that would molecule more reactive, compared with DNA.
attack DNA. The small grooves in the helix RNA is not stable under alkaline conditions, plus
also serve as protection, providing minimal the large grooves in the molecule make it
space for enzymes to attach. susceptible to enzyme attack. RNA is constantly
produced, used, degraded, and recycled.
Ultraviolet DNA is susceptible to UV damage. Compared with DNA, RNA is relatively resistant
Damage to UV damage.
(video: https://rb.gy/hgbjq2)

DNA and RNA Evolution (https://cutt.ly/IgetpSU)

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There is some evidence DNA may have occurred first, but most scientists believe RNA
evolved before DNA. RNA has a simpler structure and is needed in order for DNA to function. Also,
RNA is found in prokaryotes, which are believed to precede eukaryotes. RNA on its own can act as
a catalyst for certain chemical reactions.
The real question is why DNA evolved if RNA existed. The most likely answer for this is that
having a double-stranded molecule helps protect the genetic code from damage. If one strand is
broken, the other strand can serve as a template for repair. Proteins surrounding DNA also confer
additional protection against enzymatic attack.

LEARNING CONTENTS III. DNA Replication and Protein Synthesis

III. DNA replication (https://rb.gy/7vnygy)

The process of DNA duplication is called DNA replication. Before a cell duplicates or divides,
through either mitosis or meiosis, DNA must be replicated to ensure that each new cell receives the
correct number of chromosomes. This process occurs in all living organisms and is the basis for
biological inheritance. Replication follows several steps that involve multiple proteins called replication
enzymes and RNA.
In eukaryotic cells, such as animal cells and plant cells, DNA replication occurs in the S phase
of interphase during the cell cycle. The process of DNA replication is vital for cell growth, repair, and
reproduction in organisms.
DNA replication occurs in several steps that involve multiple proteins called replication
enzymes, as well as RNA. DNA replication is vital for cell growth, repair, and reproduction in
organisms (https://rb.gy/xvwycz).

There are three main steps to DNA replication: initiation, elongation, and termination
(https://rb.gy/4k5zq1).

Step 1: Preparation for Replication - Replication Fork Formation

Before DNA can be replicated, the double stranded molecule must be “unzipped” into two
single strands. DNA has four bases called adenine (A), thymine (T), cytosine (C) and guanine
(G) that form pairs between the two strands. Adenine only pairs with thymine and cytosine only binds
with guanine.
In order to unwind DNA, these interactions between base pairs must be broken. This is
performed by an enzyme known as DNA helicase. DNA helicase disrupts the hydrogen
bonding between base pairs to separate the strands into a Y shape known as the replication fork.
This area will be the template for replication to begin.
DNA is directional in both strands, signified by a 5' and 3' end. This notation signifies which
side group is attached the DNA backbone. The 5' end has a phosphate (P) group attached, while
the 3' end has a hydroxyl (OH) group attached. This directionality is important for replication as it only
progresses in the 5' to 3' direction. However, the replication fork is bi-directional; one strand is oriented
in the 3' to 5' direction (leading strand) while the other is oriented 5' to 3' (lagging strand). The two
sides are therefore replicated with two different processes to accommodate the directional difference.

Step 2: Replication Begins - Primer Binding

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The leading strand is the simplest to replicate. Once the DNA strands have been separated,
a short piece of RNA called a primer binds to the 3' end of the strand. The primer always binds as
the starting point for replication. Primers are generated by the enzyme DNA primase.
Video: (https://rb.gy/78ccjf)

Step 3: Elongation
Enzymes known as DNA polymerases are responsible creating the new strand by a process
called elongation. There are five different known types of DNA polymerases in bacteria and human
cells. In bacteria such as E. coli, polymerase III is the main replication enzyme, while polymerase I,
II, IV and V are responsible for error checking and repair.
DNA polymerase III binds to the strand at the site of the primer and begins adding new base
pairs complementary to the strand during replication. In eukaryotic cells, polymerases alpha, delta,
and epsilon are the primary polymerases involved in DNA replication. Because replication proceeds
in the 5' to 3' direction on the leading strand, the newly formed strand is continuous.
The lagging strand begins replication by binding with multiple primers. Each primer is only
several bases apart. DNA polymerase then adds pieces of DNA, called Okazaki fragments, to the
strand between primers. This process of replication is discontinuous as the newly created fragments
are disjointed.

Step 4: Termination
Once both the continuous and discontinuous strands are formed, an enzyme
called exonuclease removes all RNA primers from the original strands. These primers are then
replaced with appropriate bases. Another exonuclease “proofreads” the newly formed DNA to check,
remove and replace any errors.
Another enzyme called DNA ligase joins Okazaki fragments together forming a single unified
strand. The ends of the linear DNA present a problem as DNA polymerase can only add nucleotides
in the 5′ to 3′ direction. The ends of the parent strands consist of repeated DNA sequences called
telomeres. Telomeres act as protective caps at the end of chromosomes to prevent nearby
chromosomes from fusing.
A special type of DNA polymerase enzyme called telomerase catalyzes the synthesis of
telomere sequences at the ends of the DNA. Once completed, the parent strand and its
complementary DNA strand coils into the familiar double helix shape. In the end, replication produces
two DNA molecules, each with one strand from the parent molecule and one new strand.
Video (https://rb.gy/eyn054)

Replication Enzymes
DNA replication would not occur without enzymes that catalyze various steps in the process.
Enzymes that participate in the eukaryotic DNA replication process include:
 DNA helicase - unwinds and separates double stranded DNA as it moves along the DNA. It
forms the replication fork by breaking hydrogen bonds between nucleotide pairs in DNA.

 DNA primase - a type of RNA polymerase that generates RNA primers. Primers are short
RNA molecules that act as templates for the starting point of DNA replication.

 DNA polymerases - synthesize new DNA molecules by adding nucleotides to leading and
lagging DNA strands.

 Topoisomerase or DNA Gyrase - unwinds and rewinds DNA strands to prevent the DNA
from becoming tangled or supercoiled.

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 Exonucleases - group of enzymes that remove nucleotide bases from the end of a DNA
chain.

 DNA ligase - joins DNA fragments together by forming phosphodiester bonds between
nucleotides.

DNA Replication Summary (video: https://rb.gy/za5p11)

1. DNA replication is the production of identical DNA helices from a single double-stranded DNA
molecule. Each molecule consists of a strand from the original molecule and a newly formed
strand.
2. Prior to replication, the DNA uncoils and strands separate.
3. A replication fork is formed which serves as a template for replication.
4. Primers bind to the DNA and DNA polymerases add new nucleotide sequences in the 5′ to 3′
direction.
5. This addition is continuous in the leading strand and fragmented in the lagging strand. Once
elongation of the DNA strands is complete, the strands are checked for errors, repairs are made,
and telomere sequences are added to the ends of the DNA.

Key Concepts to remember

 Deoxyribonucleic acid, commonly known as DNA, is a nucleic acid that has three main
components: a deoxyribose sugar, a phosphate, and a nitrogenous base.

 Since DNA contains the genetic material for an organism, it is important that it be copied when
a cell divides into daughter cells. The process that copies DNA is called replication.

 Replication involves the production of identical helices of DNA from one double-stranded
molecule of DNA.

 Enzymes are vital to DNA replication since they catalyze very important steps in the process.

 The overall DNA replication process is extremely important for both cell growth and
reproduction in organisms. It is also vital in the cell repair process.

IV. Protein Synthesis (https://rb.gy/ew6yla, https://cutt.ly/jf6b3oV, https://cutt.ly/5f6b4cf,

https://cutt.ly/zf6niZj)

The production of proteins takes place in the cells of all living things. This process is
called protein synthesis, and it actually consists of two processes — transcription and translation.
In eukaryotic cells, transcription takes place in the nucleus. During transcription, DNA is used as a
template to make a molecule of messenger RNA (mRNA). The molecule of mRNA then leaves the
nucleus and goes to a ribosome in the cytoplasm, where translation occurs. During translation,
the genetic code in mRNA is read and used to make a protein. These two processes are summed up
by the central dogma of molecular biology: DNA → RNA → Protein.

A. Transcription ()
Transcription is the first part of the central dogma of molecular biology: DNA → RNA.
It is the transfer of genetic instructions in DNA to mRNA. During transcription, a strand of
mRNA is made to complement a strand of DNA. You can see how this happens in the
diagram below.

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Overview of Transcription. Transcription uses the sequence of bases in a strand of DNA to make a
complementary strand of mRNA. Triplets are groups of three successive nucleotide bases in DNA.
Codons are complementary groups of bases in mRNA.

Steps of Transcription
Transcription takes place in three steps: initiation, elongation, and termination. The steps
are illustrated in the figure below.

1. Initiation is the beginning of transcription. It occurs when the enzyme RNA polymerase
binds to a region of a gene called the promoter. This signals the DNA to unwind so
the enzyme can “read” the bases in one of the DNA strands. The enzyme is ready to make
a strand of mRNA with a complementary sequence of bases.

2. Elongation is the addition of nucleotides to the mRNA strand.

3. Termination is the ending of transcription. The mRNA strand is complete, and it detaches
from DNA.

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Steps of Transcription. Transcription occurs in three steps: initiation, elongation, and termination.

Processing mRNA
In eukaryotes, the new mRNA is not yet ready for translation. At this stage, it is called pre-
mRNA, and it must go through more processing before it leaves the nucleus as mature mRNA.
The processing may include splicing, editing, and polyadenylation. These processes modify the
mRNA in various ways. Such modifications allow a single gene to be used to make more than
one protein.
 Splicing removes introns from mRNA, as shown in the diagram below. Introns are
regions that do not code for the protein. The remaining mRNA consists only of regions
called exons that do code for the protein. The ribonucleoproteins in the diagram are
small proteins in the nucleus that contain RNA and are needed for the splicing process.

 Editing changes some of the nucleotides in mRNA. For example, a human protein called
APOB, which helps transport lipids in the blood, has two different forms because of editing.
One form is smaller than the other because editing adds an earlier stop signal in mRNA.

 Polyadenylation adds a “tail” to the mRNA. The tail consists of a string of As (adenine
bases). It signals the end of mRNA. It is also involved in exporting mRNA from the nucleus,
and it protects mRNA from enzymes that might break it down.

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Splicing. Splicing removes introns from mRNA.

B. Translation
Translation is the second part of the central dogma of molecular biology: RNA →
Protein. It is the process in which the genetic code in mRNA is read to make a protein.
Translation is illustrated in the diagram below. After mRNA leaves the nucleus, it moves to
a ribosome, which consists of rRNA and proteins. The ribosome reads the sequence of
codons in mRNA, and molecules of tRNA bring amino acids to the ribosome in the correct
sequence.
To understand the role of tRNA, we need to know more about its structure. Each tRNA
molecule has an anticodon for the amino acid it carries. An anticodon is complementary to
the codon for an amino acid. For example, the amino acid lysine has the codon AAG, so the
anticodon is UUC. Therefore, lysine would be carried by a tRNA molecule with the anticodon
UUC. Wherever the codon AAG appears in mRNA, a UUC anticodon of tRNA temporarily
binds. While bound to mRNA, tRNA gives up its amino acid. With the help of rRNA, bonds
form between the amino acids as they are brought one by one to the ribosome, creating a
polypeptide chain. The chain of amino acids keeps growing until a stop codon is reached.

Translation. Translation of the codons in mRNA to a chain of amino acids occurs at a

ribosome. Find the different types of RNA in the diagram. What are their roles in translation?

What Happens Next?

After a polypeptide chain is synthesized, it may undergo additional processes. For
example, it may assume a folded shape due to interactions between its amino acids. It may

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also bind with other polypeptides or with different types of molecules, such
as lipids or carbohydrates. Many proteins travel to the Golgi apparatus within the cytoplasm
to be modified for the specific job they will do.

SUMMA
Summary
• Deoxyribonucleic acid, commonly known as DNA, is a nucleic acid that has three main
components: a deoxyribose sugar, a phosphate, and a nitrogenous base.
• Since DNA contains the genetic material for an organism, it is important that it be copied when a
cell divides into daughter cells. The process that copies DNA is called replication.
• Replication involves the production of identical helices of DNA from one double-stranded
molecule of DNA.
• Enzymes are vital to DNA replication since they catalyze very important steps in the process.
 Protein synthesis is the process in which cells make proteins. It occurs in two stages: transcription
and translation.

 Transcription is the transfer of genetic instructions in DNA to mRNA in the nucleus. It includes
three steps: initiation, elongation, and termination. After the mRNA is processed, it carries the
instructions to a ribosome in the cytoplasm.

 Translation occurs at the ribosome, which consists of rRNA and proteins. In translation, the
instructions in mRNA are read, and tRNA brings the correct sequence of amino acids to the
ribosome. Then, rRNA helps bonds form between the amino acids, producing a polypeptide chain.

 After a polypeptide chain is synthesized, it may undergo additional processing to form the finished
protein.

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