Introduction

Nucleic acids, and DNA in particular, are key macromolecules for the continuity
of life. DNA bears the hereditary information that’s passed on from parents to
children, providing instructions for how (and when) to make the many proteins
needed to build and maintain functioning cells, tissues, and organisms.
How DNA carries this information, and how it is put into action by cells and
organisms, is complex, fascinating, and fairly mind-blowing, and we’ll explore it
in more detail in the section on molecular biology. Here, we’ll just take a quick
look at nucleic acids from the macromolecule perspective.

Roles of DNA and RNA in cells

Nucleic acids, macromolecules made out of units called nucleotides, come in
two naturally occurring varieties: deoxyribonucleic acid (DNA) and ribonucleic
acid (RNA). DNA is the genetic material found in living organisms, all the way
from single-celled bacteria to multicellular mammals like you and me.

Some viruses use RNA, not DNA, as their genetic material, but aren’t
technically considered to be alive (since they cannot reproduce without help
from a host).

DNA in cells
In eukaryotes, such as plants and animals, DNA is found in the nucleus, a
specialized, membrane-bound vault in the cell, as well as in certain other types
of organelles (such as mitochondria and the chloroplasts of plants). In
prokaryotes, such as bacteria, the DNA is not enclosed in a membranous
envelope, although it's located in a specialized cell region called the nucleoid.

In eukaryotes, DNA is typically broken up into a number of very long, linear

pieces called chromosomes, while in prokaryotes such as bacteria, chromosomes
are much smaller and often circular (ring-shaped). A chromosome may contain
tens of thousands of genes, each providing instructions on how to make a
particular product needed by the cell.

From DNA to RNA to proteins

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Many genes encode protein products, meaning that they specify the sequence of
amino acids used to build a particular protein. Before this information can be
used for protein synthesis, however, an RNA copy (transcript) of the gene must
first be made. This type of RNA is called a messenger RNA (mRNA), as it
serves as a messenger between DNA and the ribosomes, molecular machines
that read mRNA sequences and use them to build proteins. This progression
from DNA to RNA to protein is called the “central dogma” of molecular
biology.

Importantly, not all genes encode protein products. For instance, some genes
specify ribosomal RNAs (rRNAs), which serve as structural components of
ribosomes, or transfer RNAs (tRNAs), cloverleaf-shaped RNA molecules that
bring amino acids to the ribosome for protein synthesis. Still other RNA
molecules, such as tiny microRNAs (miRNAs), act as regulators of other genes,
and new types of non-protein-coding RNAs are being discovered all the time.

Nucleotides
DNA and RNA are polymers (in the case of DNA, often very long polymers),
and are made up of monomers known as nucleotides. When these monomers
combine, the resulting chain is called a polynucleotide (poly- = "many").
Each nucleotide is made up of three parts: a nitrogen-containing ring structure
called a nitrogenous base, a five-carbon sugar, and at least one phosphate group.
The sugar molecule has a central position in the nucleotide, with the base
attached to one of its carbons and the phosphate group (or groups) attached to
another. Let’s look at each part of a nucleotide in turn.

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Image of the components of DNA and RNA, including the sugar (deoxyribose or
ribose), phosphate group, and nitrogenous base. Bases include the pyrimidine
bases (cytosine, thymine in DNA, and uracil in RNA, one ring) and the purine
bases (adenine and guanine, two rings). The phosphate group is attached to the 5'
carbon. The 2' carbon bears a hydroxyl group in ribose, but no hydroxyl (just
hydrogen) in deoxyribose.

_Image modified from "Nucleic acids: Figure 1," by OpenStax College, Biology
(CC BY 3.0)._

Nitrogenous bases
The nitrogenous bases of nucleotides are organic (carbon-based) molecules
made up of nitrogen-containing ring structures.

Why is it called a base?

Each nucleotide in DNA contains one of four possible nitrogenous bases:
adenine (A), guanine (G) cytosine (C), and thymine (T). Adenine and guanine
are purines, meaning that their structures contain two fused carbon-nitrogen
rings. Cytosine and thymine, in contrast, are pyrimidines and have a single
carbon-nitrogen ring. RNA nucleotides may also bear adenine, guanine and
cytosine bases, but instead of thymine they have another pyrimidine base called

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uracil (U). As shown in the figure above, each base has a unique structure, with
its own set of functional groups attached to the ring structure.
In molecular biology shorthand, the nitrogenous bases are often just referred to
by their one-letter symbols, A, T, G, C, and U. DNA contains A, T, G, and C,
while RNA contains A, U, G, and C (that is, U is swapped in for T).

Sugars
In addition to having slightly different sets of bases, DNA and RNA nucleotides
also have slightly different sugars. The five-carbon sugar in DNA is
called deoxyribose, while in RNA, the sugar is ribose. These two are very
similar in structure, with just one difference: the second carbon of ribose bears a
hydroxyl group, while the equivalent carbon of deoxyribose has a hydrogen
instead. The carbon atoms of a nucleotide’s sugar molecule are numbered as 1′,
2′, 3′, 4′, and 5′ (1′ is read as “one prime”), as shown in the figure above. In a
nucleotide, the sugar occupies a central position, with the base attached to its 1′
carbon and the phosphate group (or groups) attached to its 5′ carbon.

Phosphate
Nucleotides may have a single phosphate group, or a chain of up to three
phosphate groups, attached to the 5’ carbon of the sugar. Some chemistry
sources use the term “nucleotide” only for the single-phosphate case, but in
molecular biology, the broader definition is generally accepted
In a cell, a nucleotide about to be added to the end of a polynucleotide chain will
bear a series of three phosphate groups. When the nucleotide joins the growing
DNA or RNA chain, it loses two phosphate groups. So, in a chain of DNA or
RNA, each nucleotide has just one phosphate group.

Polynucleotide chains
A consequence of the structure of nucleotides is that a polynucleotide chain
has directionality – that is, it has two ends that are different from each other. At
the 5’ end, or beginning, of the chain, the 5’ phosphate group of the first
nucleotide in the chain sticks out. At the other end, called the 3’ end, the 3’
hydroxyl of the last nucleotide added to the chain is exposed. DNA sequences

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are usually written in the 5' to 3' direction, meaning that the nucleotide at the 5'
end comes first and the nucleotide at the 3' end comes last.
As new nucleotides are added to a strand of DNA or RNA, the strand grows at
its 3’ end, with the 5′ phosphate of an incoming nucleotide attaching to the
hydroxyl group at the 3’ end of the chain. This makes a chain with each sugar
joined to its neighbors by a set of bonds called a phosphodiester linkage.

Properties of DNA
The properties of nucleic acids include-
 Polarity- Nucleic acids exhibit polarity, which refers to the presence of a 5'
end (phosphate group) and a 3' end (hydroxyl group) in each nucleotide.
This polarity is crucial for the formation of stable structures and the
replication, transcription, and translation processes.
The 5' end of one strand is linked to the 3' end of the other strand in a DNA
molecule, forming a double helix.

During replication, the two strands of DNA separate, and each strand serves as a
template for the synthesis of a new complementary strand.
The 5' to 3' directionality is maintained during this process, ensuring the accurate
replication of genetic information.

Similarly, during transcription, the 5' to 3' directionality is preserved as an RNA

polymerase enzyme synthesizes an RNA molecule complementary to a DNA
template.

The 5' end of the RNA molecule serves as the initiation site for translation, the
process by which the genetic information encoded in the RNA is translated into
a protein.

 Base pairing- Base pairing is another essential property of nucleic acids. It

refers to the specific binding between complementary nitrogenous bases in
nucleotides. In DNA, adenine (A) pairs with thymine (T) via two hydrogen
bonds, and guanine (G) pairs with cytosine (C) via three hydrogen bonds.

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 This specific pairing ensures the accurate replication and transcription of
genetic information.

Similarly, in RNA, adenine (A) pairs with uracil (U) via two hydrogen bonds,
while guanine (G) pairs with cytosine (C) via three hydrogen bonds. This base
pairing is the foundation for the formation of stable nucleic acid structures and
the accurate transmission of genetic information.

Base pairing is a critical property of nucleic acids, ensuring the accurate

replication, transcription, and translation of genetic information. The specific
pairing of complementary nitrogenous bases forms the basis for the formation of
stable nucleic acid structures and the accurate transmission of genetic
information.

For instance, if you know that the sequence of one strand is 5’-AATTGGCC-3’,
the complementary strand must have the sequence 3’-TTAACCGG-5’. This
allows each base to match up with its partner:

5'-AATTGGCC-3' 3'-TTAACCGG-5'
These two strands are complementary, with each base in one sticking to its
partner on the other. The A-T pairs are connected by two hydrogen bonds, while
the G-C pairs are connected by three hydrogen bonds.
When two DNA sequences match in this way, such that they can stick to each
other in an antiparallel fashion and form a helix, they are said to
be complementary.

 genetic information storage- The sequence of nucleotides in DNA and RNA

encodes genetic information for protein synthesis and cellular functions.
DNA serves as the repository of genetic information, storing the instructions
required for the development, functioning, and reproduction of organisms. The

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sequence of nucleotides in DNA determines the genetic code, with specific
sequences encoding the amino acid sequence of proteins.

RNA, on the other hand, plays diverse roles in gene expression. mRNA
(messenger RNA) carries genetic information from DNA to ribosomes, where
protein synthesis occurs. tRNA (transfer RNA) facilitates protein synthesis by
bringing amino acids to the ribosome and translating the genetic code into
functional proteins through the process of translation. Various types of
regulatory RNAs are involved in gene regulation and cellular processes.

The sequence of nucleotides in DNA and RNA encodes the genetic information
necessary for protein synthesis and cellular functions.

 Stability- DNA’s remarkable stability, is also primarily due to the hydrogen

bonding between complementary base pairs in DNA. DNA is more stable
than RNA due to the presence of deoxyribose sugar and thymine. This
stability is crucial for maintaining the integrity of the genetic code during
processes such as DNA replication and transcription.

Hydrogen bonding between complementary bases holds DNA strands together

in a double helix of antiparallel strands. Thymine forms two hydrogen bonds
with adenine, and guanine forms three hydrogen bonds with cytosine.
Image modified from OpenStax Biology.

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Properties of RNA
Ribonucleic acid (RNA), unlike DNA, is usually single-stranded. A nucleotide
in an RNA chain will contain ribose (the five-carbon sugar), one of the four
nitrogenous bases (A, U, G, or C), and a phosphate group. Here, we'll take a
look at four major types of RNA: messenger RNA (mRNA), ribosomal RNA
(rRNA), transfer RNA (tRNA), and regulatory RNAs.
Messenger RNA (mRNA)
Messenger RNA (mRNA) is an intermediate between a protein-coding gene and
its protein product. If a cell needs to make a particular protein, the gene
encoding the protein will be turned “on,” meaning an RNA-polymerizing
enzyme will come and make an RNA copy, or transcript, of the gene’s DNA
sequence. The transcript carries the same information as the DNA sequence of
its gene. However, in the RNA molecule, the base T is replaced with U. For
instance, if a DNA coding strand has the sequence 5’-AATTGCGC-3’, the
sequence of the corresponding RNA will be 5’-AAUUGCGC-3’.
Once an mRNA has been produced, it will associate with a ribosome, a
molecular machine that specializes in assembling proteins out of amino acids.
The ribosome uses the information in the mRNA to make a protein of a specific
sequence, “reading out” the mRNA’s nucleotides in groups of three
(called codons) and adding a particular amino acid for each codon.

Image of a ribosome (made of proteins and rRNA) bound to an mRNA, with

tRNAs bringing amino acids to be added to the growing chain. The tRNA that
binds, and thus the amino acid that's added, at a given moment is determined by
the sequence of the mRNA that is being "read" at that time.
Image credit: OpenStax Biology.
Ribosomal RNA (rRNA) and transfer RNA (tRNA)

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Ribosomal RNA (rRNA) is a major component of ribosomes, where it helps
mRNA bind in the right spot so its sequence information can be read out. Some
rRNAs also act as enzymes, meaning that they help accelerate (catalyze)
chemical reactions – in this case, the formation of bonds that link amino acids to
form a protein. RNAs that act as enzymes are known as ribozymes.
Transfer RNAs (tRNAs) are also involved in protein synthesis, but their job is to
act as carriers – to bring amino acids to the ribosome, ensuring that the amino
acid added to the chain is the one specified by the mRNA. Transfer RNAs
consist of a single strand of RNA, but this strand has complementary segments
that stick together to make double-stranded regions. This base-pairing creates a
complex 3D structure important to the function of the molecule.

Structure of a tRNA. The overall molecule has a shape somewhat like an L.

Image modified from Protein Data Bank (work of the U.S. government).

Regulatory RNA (miRNAs and siRNAs)

Some types of non-coding RNAs (RNAs that do not encode proteins) help
regulate the expression of other genes. Such RNAs may be called regulatory
RNAs. For example, microRNAs (miRNAs) and small interfering
RNAs siRNAs are small regulatory RNA molecules about 22 nucleotides long.
They bind to specific mRNA molecules (with partly or fully complementary
sequences) and reduce their stability or interfere with their translation, providing
a way for the cell to decrease or fine-tune levels of these mRNAs.
These are just some examples out of many types of noncoding and regulatory
RNAs. Scientists are still discovering new varieties of noncoding RNA.

More about regulatory RNAs

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Summary: Features of DNA and RNA
DNA RNA

Function Repository of Involved in protein synthesis and gene

genetic information regulation; carrier of genetic information in
some viruses

Sugar Deoxyribose Ribose

Structur Double helix Usually single-stranded

e

Bases C, T, A, G C, U, A, G
Table modified from OpenStax Biology.

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Questions:

1. What are the three main components of a nucleotide?

2. What are the four nitrogenous bases found in DNA?
3. What is the complementary base pairing in DNA?
4. How does the structure of RNA differ from DNA?
5. What is the role of RNA in protein synthesis?
6. What is the significance of polarity in nucleic acids?
7. What is the directionality of nucleic acid synthesis during replication and
transcription?
8. How does base pairing ensure the accurate transmission of genetic
information?
9. What is the role of DNA in storing genetic information?
10. What are the different types of RNA involved in gene expression?
11. What makes DNA more stable than RNA?
12. How does replication ensure the accurate transmission of genetic
information?
13. What is the role of transcription in gene expression?
14. What are the three main components of a nucleotide in RNA?
15. What are the four nitrogenous bases found in RNA?
16. How do the complementary base pairs differ between DNA and RNA?
17. What is the significance of the double-helix structure of DNA?
18. How do nucleic acids exhibit polarity, and what is its importance?
19. What is the role of the 5' end of an RNA molecule in translation?
20. What are the key properties of nucleic acids that ensure the accurate
transmission of genetic information?

Answers:

1. A nitrogenous base, a pentose sugar, and a phosphate group.

2. Adenine, thymine, cytosine, and guanine.
3. Adenine pairs with thymine, and guanine pairs with cytosine.
4. RNA typically exists as a single-stranded molecule, while DNA is a double-
stranded helical molecule.
5. RNA carries genetic information from DNA to ribosomes, where protein
synthesis occurs.
6. Polarity refers to the presence of a 5' end (phosphate group) and a 3' end
(hydroxyl group) in each nucleotide, which is crucial for the formation of
stable structures and the replication, transcription, and translation processes.
7. The 5' to 3' directionality is maintained during replication and transcription.
8. Base pairing ensures the accurate replication and transcription of genetic
information by forming stable nucleic acid structures.
9. DNA serves as the repository of genetic information, storing the instructions
required for the development, functioning, and reproduction of organisms.
10. mRNA, tRNA, and various regulatory RNAs are involved in gene
expression.
11. DNA is more stable than RNA due to the presence of deoxyribose sugar and
thymine.

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12. Replication ensures the accurate transmission of genetic information during
cell division by using each DNA strand as a template for the synthesis of a
new complementary strand.
13. Transcription converts the genetic information in DNA into RNA, which is
then used for protein synthesis.
14. A nitrogenous base, a ribose sugar, and a phosphate group.
15. Adenine, uracil, cytosine, and guanine.
16. In DNA, adenine pairs with thymine, and guanine pairs with cytosine. In
RNA, adenine pairs with uracil, and guanine pairs with cytosine.
17. The double-helix structure of DNA facilitates the precise replication and
transmission of genetic information during cell division.
18. Nucleic acids exhibit polarity, with a 5' end (phosphate group) and a 3' end
(hydroxyl group) in each nucleotide. This polarity is crucial for the
formation of stable structures and the replication, transcription, and
translation processes.
19. The 5' end of the RNA molecule serves as the initiation site for translation,
the process by which the genetic information encoded in the RNA is
translated into a protein.
20. Key properties of nucleic acids that ensure the accurate transmission of
genetic information include polarity, base pairing, genetic information
storage, and stability.

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Nucleic Acid Metabolism:
Nucleic acid metabolism involves creating, maintaining, and breaking down
nucleic acids.
It ensures that cells have the nucleotides they need to build DNA and RNA,
accurately replicate and transcribe genetic information, and recycle or dispose of
unused nucleotides.

Key processes include

Nucleotide Synthesis: Making the building blocks.
DNA Replication: Copying DNA.
Transcription: Making RNA from DNA.
RNA Processing: Modifying RNA.
Nucleotide Degradation: Breaking down nucleotides.

1. Nucleotide Synthesis
There are two main pathways to create nucleotides:

De Novo Synthesis: Building nucleotides from scratch using simple molecules.

For purines (adenine and guanine), the process starts with ribose-5-phosphate.
For pyrimidines (cytosine, thymine, and uracil), the process begins with a
molecule called carbamoyl phosphate.

Salvage Pathway: Recycling existing nucleotides from degraded nucleic acids.

Enzymes help attach free bases (adenine, guanine, etc.) to ribose or deoxyribose.

2. DNA Replication
This is the process of copying the entire DNA before cell division. Key steps
include:
Unwinding the DNA: Enzymes like helicase open up the double helix.
Building the new strands: DNA polymerase adds complementary nucleotides to
each original strand.
Proofreading and fixing errors: Ensuring accuracy in the new DNA.

3. Transcription
Transcription is making RNA from DNA. Here’s how it works:
Initiation: RNA polymerase binds to a specific DNA region called a promoter.
Elongation: RNA polymerase reads the DNA and adds complementary RNA
nucleotides (A with U, T with A, C with G, and G with C).
Termination: RNA polymerase reaches a stop signal and releases the RNA
strand.

4. RNA Processing
Before RNA can be used to make proteins, it often needs to be processed:
Capping: Adding a special nucleotide to the 5’ end of the RNA.
Polyadenylation: Adding a tail of adenine nucleotides to the 3’ end.
Splicing: Removing non-coding regions (introns) and joining coding regions
(exons).

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Other types of RNA, such as tRNA and rRNA, also undergo processing to
achieve their final functional form.
4a. RNA Modification: Post-transcriptional modifications play a crucial role in
regulating RNA stability, localization, and function. These modifications can
include methylation, pseudouridylation, and editing, and they often occur in
specific nucleotides within the RNA sequence. RNA modification enzymes are
responsible for catalyzing these reactions, which can impact various aspects of
gene expression and cellular physiology.
4b. RNA Turnover: RNA molecules have finite lifespans within the cell and
are subject to degradation once they have fulfilled their function. Ribonucleases
(RNases) are responsible for catalyzing the degradation of RNA molecules,
which can occur through exonucleolytic or endonucleolytic cleavage pathways.
RNA turnover is tightly regulated and can be influenced by factors such as RNA
stability elements and cellular signaling
5. Nucleotide Degradation
When nucleotides are no longer needed, they are broken down. The bases,
sugars, and phosphates can be reused or further broken down and excreted.
DNA and RNA degradation: Enzymes called nucleases cut nucleic acids into
smaller pieces.
Nucleotide breakdown: Further enzymes break down the pieces into bases,
sugars, and phosphates.

6. Epigenetic Regulation: Nucleic acid metabolism is intricately linked to

epigenetic regulation, which refers to heritable changes in gene expression that
occur independently of alterations to the DNA sequence. Epigenetic
modifications, such as DNA methylation and histone acetylation, play a crucial
role in regulating chromatin structure and accessibility, thereby influencing gene
expression patterns and cellular identity.

Dysfunction in nucleic acid metabolism can lead to a wide range of diseases,

including cancer, neurodegenerative disorders, and genetic syndromes,
highlighting the importance of understanding these processes in both health and
disease.

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What is DNA Replication?
DNA replication is the process by which a cell makes an exact copy of its DNA.
This is essential before a cell divides, so that each new cell has the same genetic
information.

The Basic Steps of DNA Replication

DNA replication can be divided into several key steps:
1. Initiation
2. Elongation
3. Termination

1. Initiation: This is the beginning phase where the replication process starts.
Key Points:
Origin of Replication: DNA replication begins at specific locations on the
DNA molecule called origins of replication.
Unwinding the DNA: Enzymes called helicases unwind the double helix
structure of DNA, creating two single strands. This area is known as the
replication fork.
Stabilizing Single Strands: Single-strand binding proteins (SSBs) attach to the
single DNA strands to prevent them from re-annealing (coming back together).
2. Elongation: This phase involves the synthesis of new DNA strands.
Key Points:
Primase and RNA Primer: The enzyme primase creates a short RNA segment
called a primer, which provides a starting point for DNA synthesis.
DNA Polymerase: This is the main enzyme that adds new nucleotides to the
growing DNA strand. DNA polymerase can only add nucleotides to an existing
strand, which is why the primer is necessary.
Leading and Lagging Strands: DNA polymerase works continuously on one
strand (the leading strand) in the same direction as the replication fork. On the
other strand (the lagging strand), DNA synthesis occurs in short segments called
Okazaki fragments, moving away from the replication fork. These fragments are
later joined together by an enzyme called DNA ligase.

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Directionality: DNA polymerase can only add nucleotides in one direction (5'
to 3'). This means that the two new strands are synthesized in opposite
directions.
3. Termination: This phase wraps up the replication process.
Key Points:
Removing RNA Primers: The RNA primers are removed, and the gaps are
filled with DNA nucleotides.
Sealing the Gaps: DNA ligase seals any remaining gaps between the Okazaki
fragments on the lagging strand, creating a continuous strand.

Detailed Steps in DNA Replication

Helicase Unwinds DNA: The helicase enzyme unwinds the double-stranded
DNA into two single strands by breaking the hydrogen bonds between the base
pairs (A-T and C-G).
Single-Strand Binding Proteins (SSBs) Stabilize the Single Strands: These
proteins bind to the separated strands to keep them apart and prevent them from
re-annealing.
Primase Lays Down RNA Primers: Primase synthesizes short RNA primers
complementary to the DNA template. These primers serve as starting points for
DNA synthesis.
DNA Polymerase Starts Adding Nucleotides: DNA polymerase adds DNA
nucleotides to the 3' end of the RNA primer, creating a new DNA strand that is
complementary to the template strand.
Leading Strand Synthesis: On the leading strand, DNA polymerase synthesizes
DNA continuously in the direction of the replication fork.
Lagging Strand Synthesis: On the lagging strand, DNA polymerase synthesizes
DNA in short segments (Okazaki fragments) away from the replication fork.
RNA Primers are Replaced with DNA: Once the DNA has been synthesized, the
RNA primers are removed and replaced with DNA nucleotides by another DNA
polymerase.

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DNA Ligase Seals the Fragments: DNA ligase joins the Okazaki fragments on
the lagging strand, creating a continuous DNA strand.

Ensuring Accuracy
During DNA replication, the cell has mechanisms to ensure that the process is
accurate:

Proofreading: DNA polymerase has a proofreading function that checks for

errors and corrects them immediately.
Mismatch Repair: After replication, other enzymes can correct any remaining
errors.

Summary
DNA replication is a critical process that allows cells to divide and pass genetic
information to their offspring. It involves:
Initiation: Starting at the origin of replication, unwinding the DNA, and
stabilizing the single strands.
Elongation: Synthesizing new DNA strands using primase, DNA polymerase,
and creating leading and lagging strands.
Termination: Removing RNA primers, filling in gaps, and sealing the DNA
fragments.

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DNA replication is essential for cellular proliferation, genetic stability, and
inheritance for several reasons:
1. Cellular Proliferation: DNA replication is necessary for cell division and
proliferation. Before a cell divides, it must replicate its DNA to ensure that each
daughter cell receives a complete set of genetic information.
2. Genetic Stability: Accurate DNA replication is crucial for maintaining genetic
stability and preventing mutations. DNA polymerases have proofreading
capabilities that help ensure the fidelity of DNA synthesis, and DNA repair
mechanisms are in place to correct errors that may occur during replication.
3. Inheritance: DNA replication is central to the process of inheritance, ensuring
that genetic information is faithfully passed from one generation to the next. By
faithfully replicating the genome, DNA replication ensures that offspring inherit
genetic traits from their parents.

DNA replication is a highly orchestrated process involving multiple enzymes

and proteins that ensures the faithful duplication of the genetic material. Its
semi-conservative nature, along with the involvement of key enzymes such as

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DNA polymerase, helicase, primase, and DNA ligase, is essential for cellular
proliferation, genetic stability, and inheritance.

What is RNA Transcription?

Transcription is the first step in gene expression. It involves copying a gene's
DNA sequence to make an RNA molecule.
Transcription is performed by enzymes called RNA polymerases, which link
nucleotides to form an RNA strand (using a DNA strand as a template).

Transcription has three stages: initiation, elongation, and termination.

In eukaryotes, RNA molecules must be processed after transcription: they

are spliced and have a 5' cap and poly-A tail put on their ends.

Transcription is controlled separately for each gene in your genome. Have you
ever had to transcribe something? Maybe someone left a message on your
voicemail, and you had to write it down on paper. Or maybe you took notes in
class, then rewrote them neatly to help you review. As these examples
show, transcription is a process in which information is rewritten. Transcription
is something we do in our everyday lives, and it's also something our cells must
do, in a more specialized and narrowly defined way.

In biology, transcription is the process of copying out the DNA sequence of a

gene in the similar alphabet of RNA.

Overview of transcription
Transcription is the first step in gene expression, in which information from
a gene is used to construct a functional product such as a protein. The goal of
transcription is to make a RNA copy of a gene's DNA sequence. For a protein-
coding gene, the RNA copy, or transcript, carries the information needed to
build a polypeptide (protein or protein subunit). Eukaryotic transcripts need to
go through some processing steps before translation into proteins.

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In transcription, a region of DNA opens up. One strand, the template strand,
serves as a template for synthesis of a complementary RNA transcript. The other
strand, the coding strand, is identical to the RNA transcript in sequence, except
that it has uracil (U) bases in place of thymine (T) bases.

Example:
Coding strand: 5'-ATGATCTCGTAA-3' Template strand: 3'-
TACTAGAGCATT-5' RNA transcript: 5'-AUGAUCUCGUAA-3'
For a protein-coding gene, the RNA transcript contains the information needed
to synthesize a polypeptide (protein or protein subunit) with a particular amino
acid sequence. In this case:

RNA transcript (acting as messenger RNA): 5'-AUGAUCUCGUAA-3'

Polypeptide: Met-Ile-Ser-STOP

RNA polymerase
The main enzyme involved in transcription is RNA polymerase, which uses a
single-stranded DNA template to synthesize a complementary strand of RNA.
Specifically, RNA polymerase builds an RNA strand in the 5' to 3' direction,
adding each new nucleotide to the 3' end of the strand.

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RNA polymerase synthesizes an RNA strand complementary to a template DNA
strand. It synthesizes the RNA strand in the 5' to 3' direction, while reading the
template DNA strand in the 3' to 5' direction. The template DNA strand and
RNA strand are antiparallel.

RNA transcript: 5'-UGGUAGU...-3' (dots indicate where nucleotides are still

being added at 3' end) DNA template: 3'-ACCATCAGTC-5'

Stages of transcription
Transcription of a gene takes place in three stages: initiation, elongation, and
termination. Here, we will briefly see how these steps happen in bacteria. You
can learn more about the details of each stage (and about how eukaryotic
transcription is different) in the stages of transcription article.

Initiation. RNA polymerase binds to a sequence of DNA called the promoter,

found near the beginning of a gene. Each gene (or group of co-transcribed genes,
in bacteria) has its own promoter. Once bound, RNA polymerase separates the
DNA strands, providing the single-stranded template needed for transcription.

The promoter region comes before (and slightly overlaps with) the transcribed
region whose transcription it specifies. It contains recognition sites for RNA

21
polymerase or its helper proteins to bind to. The DNA opens up in the promoter
region so that RNA polymerase can begin transcription.

Elongation. One strand of DNA, the template strand, acts as a template for RNA
polymerase. As it "reads" this template one base at a time, the polymerase builds
an RNA molecule out of complementary nucleotides, making a chain that grows
from 5' to 3'. The RNA transcript carries the same information as the non-
template (coding) strand of DNA, but it contains the base uracil (U) instead of
thymine (T).

What do 5' and 3' mean?

RNA polymerase synthesizes an RNA transcript complementary to the DNA

template strand in the 5' to 3' direction. It moves forward along the template
strand in the 3' to 5' direction, opening the DNA double helix as it goes. The
synthesized RNA only remains bound to the template strand for a short while,
then exits the polymerase as a dangling string, allowing the DNA to close back
up and form a double helix.

In this example, the sequences of the coding strand, template strand, and RNA
transcript are:
Coding strand: 5' - ATGATCTCGTAA-3'
Template strand: 3'-TACTAGAGCATT-5'
RNA: 5'-AUGAUC...-3' (the dots indicate where nucleotides are still being
added to the RNA strand at its 3' end)

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Termination. Sequences called terminators signal that the RNA transcript is
complete. Once they are transcribed, they cause the transcript to be released
from the RNA polymerase. An example of a termination mechanism involving
formation of a hairpin in the RNA is shown below.

The terminator DNA encodes a region of RNA that forms a hairpin structure
followed by a string of U nucleotides. The hairpin structure in the transcript
causes the RNA polymerase to stall. The U nucleotides that come after the
hairpin form weak bonds with the A nucleotides of the DNA template, allowing
the transcript to separate from the template and ending transcription.

Eukaryotic RNA modifications

In bacteria, RNA transcripts can act as messenger RNAs (mRNAs) right away.
In eukaryotes, the transcript of a protein-coding gene is called a pre-mRNA and
must go through extra processing before it can direct translation.

Eukaryotic pre-mRNAs must have their ends modified, by addition of a 5'

cap (at the beginning) and 3' poly-A tail (at the end).

Many eukaryotic pre-mRNAs undergo splicing. In this process, parts of the pre-
mRNA (called introns) are chopped out, and the remaining pieces (called exons)
are stuck back together.

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Top of image: Diagram of a pre-mRNA with a 5' cap and 3' poly-A tail. The 5'
cap is on the 5' end of the pre-mRNA and is a modified G nucleotide. The poly-
A tail is on the 3' end of the pre-mRNA and consists of a long string of A
nucleotides (only a few of which are shown).

The pre-mRNA still contains both exons and introns. Along the length of the
mRNA, there is an alternating pattern of exons and introns: Exon 1 - Intron 1 -
Exon 2 - Intron 2 - Exon 3. Each consists of a stretch of RNA nucleotides.

During splicing, the introns are removed from the pre-mRNA, and the exons are
stuck together to form a mature mRNA.

Bottom of image: Mature mRNA that does not contain the intron sequences
(Exon 1 - Exon 2 - Exon 3 only).

End modifications increase the stability of the mRNA, while splicing gives the
mRNA its correct sequence. (If the introns are not removed, they'll be translated
along with the exons, producing a "gibberish" polypeptide.)

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20 questions and answers on nucleic acid metabolism:
Questions:
1. What are the key processes involved in nucleic acid metabolism?
2. What is the significance of DNA replication in cellular proliferation, genetic
stability, and inheritance?
3. Describe the semi-conservative nature of DNA replication.
4. What are the main steps involved in the DNA replication process?
5. What is the role of DNA repair mechanisms in maintaining genomic
integrity?
6. Explain the process of transcription and the different stages involved.
7. How do transcription factors regulate gene expression?
8. What are the three main post-transcriptional modifications of RNA
molecules?
9. How do capping, splicing, and polyadenylation influence RNA stability,
localization, and translational efficiency?
10. What is the difference between exonucleolytic and endonucleolytic
degradation of nucleic acids?
11. Describe the key functions of exonucleases and endonucleases in nucleic
acid metabolism.
12. What are the potential consequences of dysregulation in nucleic acid
metabolism?
13. How is nucleotide metabolism regulated, and what is its importance?
14. Explain the role of epigenetic modifications in the regulation of nucleic acid
metabolism.
15. What are the different types of DNA repair pathways, and how do they
maintain genomic stability?
16. Describe the process of RNA processing, including the removal of introns
and the addition of the 5' cap and 3' poly(A) tail.
17. How do RNA modifications, such as methylation and editing, influence
RNA function and stability?
18. What is the significance of the 5' to 3' directionality in nucleic acid synthesis
and its importance in replication and transcription?
19. Explain the concept of RNA turnover and the role of ribonucleases in this
process.

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20. Discuss the links between nucleic acid metabolism and cellular homeostasis,
highlighting the importance of these processes in health and disease.

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Answers:
1. Key processes include DNA replication, RNA transcription, mRNA
translation, DNA repair, RNA processing, RNA modification, and nucleotide
metabolism.
2. DNA replication is essential for cellular proliferation, genetic stability, and
inheritance, as it ensures accurate duplication of the genetic material and its
transmission to daughter cells.
3. DNA replication is semi-conservative, meaning that each newly synthesized
DNA molecule contains one parental strand and one newly synthesized strand.
4. The main steps are initiation, unwinding, primer synthesis, DNA synthesis,
ligating Okazaki fragments, and termination.
5. DNA repair mechanisms, such as base excision repair, nucleotide excision
repair, mismatch repair, and double-strand break repair, correct errors and
maintain genomic integrity.
6. Transcription involves initiation, elongation, and termination, with RNA
polymerase synthesizing RNA complementary to the DNA template.
7. Transcription factors can act as activators or repressors to regulate the activity
of RNA polymerase and the initiation of transcription.
8. The three main post-transcriptional modifications are capping, splicing, and
polyadenylation.
9. These modifications enhance RNA stability, facilitate nuclear export, and
regulate translation efficiency.
10. Exonucleases degrade nucleic acids from the ends, while endonucleases
cleave at internal phosphodiester bonds.
11. Exonucleases are involved in DNA repair, RNA turnover, and degradation of
foreign nucleic acids, while endonucleases play roles in DNA repair, RNA
processing, and defense against foreign nucleic acids.
12. Dysregulation in nucleic acid metabolism can lead to genomic instability,
accumulation of aberrant RNA species, and various disease states.
13. Nucleotide metabolism involves the synthesis, salvage, and degradation of
nucleotides, and it is crucial for maintaining the availability of building blocks
for DNA and RNA synthesis.

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14. Epigenetic modifications, such as DNA methylation and histone acetylation,
can regulate chromatin structure and accessibility, thereby influencing gene
expression patterns and nucleic acid metabolism.
15. The main DNA repair pathways are base excision repair, nucleotide excision
repair, mismatch repair, and double-strand break repair.
16. RNA processing involves the removal of introns, addition of a 5' cap, and
addition of a 3' poly(A) tail.
17. RNA modifications, such as methylation and editing, can influence RNA
stability, localization, and function.
18. The 5' to 3' directionality is crucial for the accurate replication and
transcription of genetic information.
19. RNA turnover is the degradation of RNA molecules by ribonucleases, and it
is essential for regulating gene expression.
20. Nucleic acid metabolism is critical for cellular homeostasis, and its
dysregulation is linked to various disease states, highlighting the importance of
understanding these processes.

Conclusion:
In today's lecture, we delved into the dynamic nature of nucleic acid
metabolism, highlighting its critical role in regulating gene expression and
maintaining cellular function. Here are the key points covered:

Nucleic Acid Metabolism Overview: Nucleic acid metabolism encompasses the

biochemical processes involved in the synthesis, modification, and degradation
of DNA and RNA molecules. These processes are dynamic and tightly regulated
to ensure genomic integrity, proper gene expression, and cellular homeostasis.
Synthesis and Replication: DNA replication is a fundamental process in
nucleic acid metabolism, ensuring faithful duplication of the genetic material
during cell division. The semi-conservative nature of DNA replication ensures
that each daughter cell receives an identical copy of the genome, essential for
maintaining genetic stability and inheritance.
Transcription and RNA Processing: Transcription is the process of
synthesizing RNA molecules from DNA templates, a key step in gene

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expression regulation. Post-transcriptional modifications, such as capping,
splicing, and polyadenylation, play crucial roles in RNA stability, localization,
and translational efficiency, thereby influencing cellular function.
Degradation: Nucleic acid degradation pathways, mediated by nucleases,
regulate the turnover of DNA and RNA molecules, removing damaged or
unwanted genetic material and controlling gene expression. Dysregulation of
nucleic acid degradation pathways can lead to genomic instability and disease.
Understanding nucleic acid metabolism is essential in various contexts:
Health and Disease: Dysfunctions in nucleic acid metabolism can lead to a
wide range of diseases, including cancer, genetic disorders, and
neurodegenerative diseases. By understanding the underlying molecular
mechanisms, researchers can develop targeted therapies and diagnostic tools for
these conditions.
Biotechnology: Nucleic acid metabolism is central to biotechnological
applications such as gene editing, recombinant DNA technology, and mRNA-
based therapeutics.

By harnessing our knowledge of nucleic acid metabolism, scientists can

manipulate DNA and RNA molecules to engineer novel therapies, vaccines, and
diagnostic tools.

In conclusion, nucleic acid metabolism is a dynamic and essential process that

governs gene expression and cellular function. Understanding nucleic acid
metabolism is crucial for advancing biomedical research, developing new
therapies, and addressing health challenges in both health and disease contexts.

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Assignment on nucleic acids (Submit: 24/5/2024):

1. What are the four nitrogenous bases found in DNA, and how do they pair
with each other?
2. Why is DNA often described as a double helix structure? What specific
properties of nucleic acids contribute to this unique structure?
3. In DNA replication, what enzyme is responsible for synthesizing new DNA
strands, and what is its role in ensuring the accuracy of DNA replication?
4. Can you identify the differences between a purine and a pyrimidine base in
nucleic acids?
5. What is the significance of the phosphate backbone in the structure of DNA
and RNA molecules?
6. How do mutations in DNA replication or repair pathways contribute to
genetic diseases or cancer development?
7. Describe the difference in the sugar-phosphate backbone between DNA and
RNA molecules.
8. What is the role of hydrogen bonding in stabilizing the double helix structure
of DNA?
9. How does the process of transcription differ between prokaryotic and
eukaryotic cells?
10. What is the significance of the complementary base pairing rule in DNA and
RNA molecules?

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