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Subject Code CHEM 3 Chemistry 3

Module Code 5.0 Biomolecules II
Lesson Code 5.7 Review of Nucleic Acids: Structure and Functions (Part II)
Time Frame 30 minutes

TA ATA
Components Tasks
(mins) (mins)
Target At the end of this module, you are expected to:
• describe the three-dimensional structures of nucleic acids and
the interactions that stabilize them; and 1
• differentiate the nucleic acids RNA and DNA in terms of their
structure and function.
Hook With the occurrence of the COVID-19 pandemic, it is almost
imperative that people are to be made more aware of how viral
diseases spread so that measures can be implemented to prevent
their rapid spread. The development of vaccines has become an
unprecedented race against time. Much of these research efforts
are grounded on the understanding of nucleic acids.

Let’s see how you understand nucleic acid so far. Tell whether
these statements are TRUE or FALSE. (Non-graded)

_______ a) Viruses only have RNA but not DNA as their

genetic material.
_______ b) RNA can only be single stranded.
_______ c) In RNA, guanine only pairs with cytosine while
adenine only pairs with uracil.
_______ d) Genes and genomes are synonyms.
_______ e) The entirety of DNA and RNA strands are coding
sequences.

If your answer were ‘False’ in all the statements, you got it all
right! 7

Most viruses have either RNA or DNA as their genetic material

(Graham, 2014) and they require a host for the enzymes required
for certain biological processes such as replication (Poltronieri,
Sun, and Mallardo, 2015; Payne, 2017). RNA can also be double
stranded (Clancy, 2008). In RNA, guanine commonly pairs with
cytosine while adenine pairs with uracil but scientists have proven
the existence of guanine pairing with uracil in practically all
functional RNAs. This is called the G-U wobble base pair which
was later found to play important roles especially as recognition
sites in biological processes such as in protein synthesis (Varani
and McClain (2000). Genes are quite different from genomes.
Genes pertain to certain sequences in nucleic acids that code for
particular substances, mostly proteins, essential to biological
functions and characteristics. A genome is the totality of an
organism’s genetic material including the genes and the other
substances that control the activities of those genes (NIH, 2017).
In the human DNA, only less than 5% codes for proteins which
means to say that the vast majority of the nucleic acid sequences
are non-coding. Nonetheless, they play important roles in genetic

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regulation (National Research Council (US) Committee on

Mapping and Sequencing the Human Genome, 1988).

In this learning guide, we shall further explore details on nucleic

acid structures and functions, particularly those of
deoxyribonucleic acid (DNA) and ribonucleic acid (RNA).
Ignite Recall from LG 5.8 that the primary structure of nucleic acids is
formed by a string of nucleotides covalently connected to each
other by phosphodiester linkages. Stable, more complex structures
such as folding and formation of loops and helices due to the
interactions between the nucleotides in the sequence are
considered secondary structures. More complex folding of
secondary structures or interactions with other nucleotide units are
considered tertiary structures. (Nelson and Cox, 2017).

As scientists have proven that nucleic acids carry genetic

information, much research efforts were put forth towards
deciphering its structure.

Deoxyribonucleic Acid (DNA)

DNA is the genetic material of most organisms which is found

almost exclusively in the nucleus (Nelson and Cox, 2017). In the
early 1950’s, two British physicists, Maurice Wilkins and
Rosalind Franklin, obtained the first high-resolution image of
DNA fibers known as Photo 51 using x-ray diffraction technique
which proved that DNA is a double helix (Nelson & Cox, 2017).
Latychevskaia and Fink (2018) made a comprehensive
interpretation of the image (Figure 1).
14

Figure 1. Interpretation of the x-ray diffraction image of DNA

Fibers by Latychevskaia and Fink (2018). “(a) The "X"-form
distribution of the diffraction peaks which is an indication of a
helical structure. (b) The period of the helix, 34 Å, was
computed from the distance between the two intense peaks. (c)
The broad extended peaks on the top and the bottom are formed
by diffraction on small periodical features which are the base
pairs measured to be 3.4 Å apart. (d) The missing diffraction
spots is an indication of a double helix. (e) The position of the
maxima of the diffraction spots is related to the radius of the
DNA helix.” (Image retrieved from:
https://www.researchgate.net/publication/328841526)

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It was James Watson (American) and Francis Crick (British)

who pieced all discoveries together and came up with the three-
dimensional structure; that is, the secondary structure) of DNA.
In 1953, they postulated that the DNA is a double helix with the
two single polynucleotide DNA strands coiled around each other
along the same axis but in opposite directions; that is, antiparallel
(Figure 2) (Nelson and Cox, 2017). The strands are
complementary to each other and are held together by hydrogen
bonds between meticulously placed nitrogenous bases (Figure 3).
This means that the 5’ end of one strand is linked with the 3’ end
of the other strand through the purine and pyrimidine base pairs
(Figure 2). In DNA, guanine pairs with cytosine and adenine
pairs with thymine. The specificity of hydrogen bonding causes
the base sequence of one strand to dictate the base sequence of its
complementary strand (Hornback, 2006).

Figure 2. Complementary DNA strands coiled together in

opposite directions. (Image from Hornback, 2006)

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Figure 3. Hydrogen-bonding between nitrogenous bases in a

DNA double helix. (Image from McMurry, 2011)

The human DNA is quite a large molecule containing about 3

billion base pairs grouped into 23 chromosomes. Its length is about
2 meters (Hornback, 2006). The double helix is 20 Å in diameter.
One full turn or period has a length (height) of 34 Å with 10 base
pairs; thus, the distance between base pairs is 3.4 Å. In a period,
two types of grooves are present – a minor groove and a major
groove which are 6 Å and 12 Å in length, respectively (McMurry,
2011). A space-filling model of a DNA double helix is shown in
Figure 3. The three-dimensional structure of DNA like DNA
supercoils that it forms around proteins (histones) is considered its
tertiary structure.

Figure 4. A space-filling model of a DNA double helix

(Image from McMurry, 2011)

Ribonucleic Acid (RNA)

Ribonucleic acid (RNA) is the second major type of nucleic acid

which is found throughout the cell. It is the genetic material of

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several viruses. Unlike DNA, its sugar component is ribose and

instead thymine, it has uracil as one of its bases.

RNA is usually single stranded that exhibits intramolecular base-

pairing between complementary base pairs. It can undergo folding
to assume unique, complex, and irregular secondary structures
including different types of loops and double-stranded lengths
(Figure 5) (Nelson and Cox, 2011; Clancy, 2008). It can also
hybridize with other RNA strands forming double stranded helices
(Clancy, 2008).

Figure 5. Secondary structures in an RNA strand including (i)

single strands, (ii) bulge, (iii) internal loop, and hairpin loop (iv)
(Image from Hornback, 2006)

RNA has several forms and functions particularly related to gene

regulation and expression; that is, protein synthesis (Nelson and
Cox, 2017; McMurry, 2011; Clancy, 2008; Hornback, 2006).
RNAs include messenger RNA (mRNA), transfer RNA (tRNA),
and ribosomal RNA (rRNA) with different activities and
functions (Clancy, 2008) especially in translation (see Figure 6).

The Central Dogma

Gene expression is governed by the central dogma (Figure 6).

Replication is the process by which DNA copies are made from a
parent DNA. Transcription involves the synthesis of a messenger
RNA from a parent DNA strand in order to transfer genetic
information. Translation is the process by which proteins are
synthesized based on the sequence of a messenger RNA. In this
learning guide, we shall not be going through the nitty gritty of the
processes involved in the central dogma but it is worthwhile to

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note that this process has been ingeniously designed to preserve

the integrity of genetic materials as they are passed on. However,
due to several factors, chemical and physical alike, mutations or
changes in the genetic sequences are still possible.

Figure 6. The central dogma. (Image Source: Genius Media

Group Inc., 2021, Retrieved from https://genius.com/Biology-
genius-the-central-dogma-annotated)

Navigate Concept check. 😊

Graded Formative Assessment

Answer the following questions and submit your answer sheet in

accordance to the instructions of your teacher.

Part I. Choose the letter of the correct answer. (1 point each)

1. peptides and proteins: peptide bonds :: nucleic acids : ______
A. amide bonds
B. glycosidic linkages
C. phosphodiester linkages
D. salt bridges
2. Which is/are present in DNA but not in RNA?
A. –OH in the C2’ position of the pentose sugar
B. thymine
C. uracil 6
D. Both A and C
3. The sequence: 5‘-ACTCGATTACGATACGA-3ʼ is most
likely a segment of what nucleic acid?
A. DNA
B. RNA
C. both DNA and RNA
4. What DNA sequence is complementary to this nucleic acid
strand?
3ʼ-TACAATCAGATC-5ʼ
A. 3ʼ-UACAAUCAGAUC-5ʼ
B. 3ʼ-ATGTTAGTCTAG-5ʼ
C. 5ʼ-ATGTTAGTCTAG-3ʼ
D. 5ʼ-AUGUUAGUCUAG-3ʼ
E. 3ʼ-AUGUUAGUCUAG-5ʼ

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5. What RNA sequence is complementary to this nucleic acid

strand?
3ʼ-TACAATCAGATC-5ʼ
A. 3ʼ-UACAAUCAGAUC-5ʼ
B. 3ʼ-ATGTTAGTCTAG-5ʼ
C. 5ʼ-ATGTTAGTCTAG-3ʼ
D. 5ʼ-AUGUUAGUCUAG-3ʼ
E. 3ʼ-AUGUUAGUCUAG-5ʼ

Part II. Write ✓ if the statement conveys a factual/logical sense;

otherwise, write . (1 point each)
_____ 1. The complementary strands in a double helix are held
together by covalent bonds.
_____ 2. Both DNA and RNA are capable of forming double
helices.
_____ 3. Both DNA and RNA can be found in the nucleus of
cells.
_____ 4. The linkage between adenine and thymine or adenine
and uracil are stronger than that between cytosine and
guanine.
_____ 5. Adenosine diphosphate (ADP) and adenosine
triphosphate (ATP) can be derived from a
ribonucleotide.

Part III. Answer this question concisely.

Nucleic acids, despite being quite large, are soluble in water.
Explain why this is possible? (2 points)
Knot The nucleic acids, RNA and DNA, are important genetic materials
of living organisms. Like proteins, they can assume primary,
secondary, and tertiary structures. Secondary structures are held
together by H-bonds between nucleotides or nitrogenous bases.

RNA differs from DNA in that it has a ribose instead of

2
deoxyribose as its sugar component and has uracil instead of
thymine as one of its nitrogenous bases.

Though DNA is usually double stranded (double helix) and RNA

is usually single stranded, both nucleic acids can form single
strands in certain instances.
a suggested time allocation set by the teacher
b actual time spent by the student (for information purposes only)

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References:
Clancy, S. (2008) Chemical structure of RNA. Nature Education 7(1):60. Retrieved from
https://www.nature.com/scitable/topicpage/chemical-structure-of-rna-348/
Graham, B.J. (2014) Virus. NIH National Human Genome Research Institute. Retrieved from
https://www.genome.gov/genetics-glossary/Virus
Hornback, J.M. (2006). Organic Chemistry, 2nd ed. Thomson Brooks/Cole: California
Macmurry, J. (2011) Fundamentals of Organic Chemistry, 7th ed. Brooks/Cole: California.
National Research Council (US) Committee on Mapping and Sequencing the Human Genome (1998).
Mapping and Sequencing the Human Genome, Introduction, 2. Washington (DC): National
Academies Press (US), Retrieved from https://www.ncbi.nlm.nih.gov/books/NBK218247/
Nelson, D.L.; and Cox, M.M. (2017) Lehninger Principles of Biochemistry, 7th ed. W. H. Freeman
and Company: New York.
NIH National Human Genome Research Institute Studying Genes (August 2017) Studying genes.
Retrieved from https://www.nigms.nih.gov/education/Documents/Studying_genes_final.pdf
Payne, S. (2017) Chapter 28 - Introduction to DNA Viruses, Editor(s): Susan Payne, Viruses, 36,
Retrieved from https://doi.org/10.1016/B978-0-12-803109-4.00028-3.
Poltronieri, P., Sun, B., & Mallardo, M. (2015). RNA Viruses: RNA Roles in Pathogenesis,
Coreplication and Viral Load. Current genomics, 16(5), 327–335. Retrieved from
https://doi.org/10.2174/1389202916666150707160613
Varani, G., & McClain, W. H. (2000). The G- Uwobble base pair. A fundamental building block of
RNA structure crucial to RNA function in diverse biological systems. EMBO reports, 1(1),
18–23. Retrieved from https://doi.org/10.1093/embo-reports/kvd001

Prepared by: GENALYN ALICE R. VILORIA Reviewed by: MELBA C. PATACSIL

Position: Special Science Teacher V Position: Special Science Teacher V
Campus: PSHS-CVC Campus: PSHS-CARC

© 2020 Philippine Science High School System. All rights reserved. This document may contain proprietary information and may only be
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