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Nucleotides and Nucleic Acids

(DNA and RNA)

Lesson Learning Outcomes

Students should be able to:
• understand the properties of nucleotides
and nucleic acids
• recognize DNA and RNA

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From The Lesson Plan

• 7.0 Nucleic Acids Structure and Functions
• 7.1 Structures of Nucleotides (in DNA
• and RNA)
• 7.2 Polynucleotides
• 7.3 Types of RNA Molecules

• 8.0 Nucleic Acids Structure and Functions

• 8.4 Genetic Code
• 8.5 Overview of DNA Replication, Transcription and
Translation

Essential Question

What are the structures of the nucleotides?

How are nucleotides joined together to form
nucleic acids?

How is information stored in nucleic acids?

What are the biological functions of
nucleotides and nucleic acids?

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1. Introduction

DNA is the nucleic acid that

is responsible for
"programming" many of our
traits.

Where is genome located? … eukaryotic or prokaryotic cell?

Where is genome located? … eukaryotic or prokaryotic cell?

Figure 1-18a Molecular Biology of the Cell, Fifth Edition (© Garland Science 2008)

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1. Introduction

Figure 1-50 Molecular Biology of the Cell, Fifth Edition (© Garland Science 2008)

1. Introduction

Why???
Because both have mutations in the same gene (called kit),
required for the development and maintenance of pigment cells
Figure 1-53 Molecular Biology of the Cell, Fifth Edition (© Garland Science 2008)

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DNA sequence
GCAGTGAGCCAAGATTGCACCATTGCACCCCAGCCTGGGCGACAAGAGTGAAACTCCGTCTCAAAAAACA
AAAAACAAAAAAACAACTAAACAGCTGGACGCGGTGGCTCAAGCCTATAATCCCAGCACTTTGGAAGGCC
GAGGCGGATGGATTACCTGAGTTCGGGAGTTCAAGACCAGCCTGACCAACATGGAGAAACCGTTTCTACT
AAAAATACAAAATTGGCTGGGCATGGTGGCCCATGCCTGTAATCCCAGCTACTCAGGAGGCTGAGGCAGG
AGAATCGCTTGAACCTGGGAGGCGGAGGTTGCAGTGAGCCAAGATCAAGCCACTGCACTCCAGCCTGGGC
TACAAAAGCGAAACTCCGTCTCAAACAAACAAAAAACAGAGCAATGGACCTGAGAGGGGACAGTGGCCAC
AAATCTTCCTACAGAAACAACCCCCTGGCATAGAGAGTGTTGCCAGTGGGTTCTACCAAAATGCAAGCAC
AAGAGAATTCCAGCCTGAAGCAAACTCTTCCTGCAGAAGGAAGAAAGGGGAACACTTCCCAAGCCACCTT
ATGGGGCCTACAGAGCCTTGGTACGGAAACCTGATGAGAAAGGCACATGGGAAAACCCATACGCCTCATT
CACACACACATGCAGATGCAGAAATCCCACACGAAATATCAGCAGGCCGGGCACAACTCACACACCCCAG
CACTTTGGGAGACCAAGGTGGGAGGAAGATTGCTTGAAATCAGGAGGTTTTTTTTTTTTTTTTTTTTAAA
GACATGGTCTCACTCTGTCACCTAGGCTGGAGTGCAGTGGCACGATCTCAGTTCACTGCAACCTCTGCCT
CTGGGCTCAAGCAATCCTCCCACCTCAGCCTCTGGAGTAGCTGGGACTACAGGTACATGCCAACACACCC
Conserved sequences
AGCTAATTTTTTGTATTTTTTGTAGAGACAGGGTTTCCCCATGTTGTCCAGGCTGCTCTTGAACTCCTGG
GCTCAAGTGATCTGCCCGCCTCAGCCTCCCAAAGTGTTGGGATTACAGGCGTGAGCCACGACGACCCACT
GACCCTGTCTCTTTAAAAAAAAAGAAGAAAACATCAGCAAACCAAATCCTGCAATGTTAAAAACGGTAGG
TTTTTTATTTACAGAATAAATACATCTGTAAATAAAAAGTTGGTTTGATATTAACAGAAAAAAATCATTG
AAATTCACCATATTAAGAGATTAAAAAAAACCTCTAAGAACTCTCTGCCTACTGCTATGTTTTGATTTTT
TAAATCTAGCAATCTTGCTCAACCCAACAGATGTAGATCAAGTGTTTCAGAAATCACCTATTCACGCTAA
AACTCTTAGCAGAGGGGGAATGCAAGGGAACTTCACTAACTTGATAAAGGGCATCTATAAAACACCATTC
TGGCTGGGCGTGGTGGCTCAAGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGGAATCGCTTGAGG
TCAGGAGTTTGAGACCAGCCTGACCAACATGGTGAAACCCCATTTCTACTAAAAATACAAAACTTAGCTG

Figure 1-22 Molecular Biology of the Cell, Fifth Edition (© Garland Science 2008)

??????

Figure 4-83 Molecular Biology of the Cell (© Garland Science 2008)

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Level of structure in nucleic acids

• In proteins – primary, secondary, tertiary and

quaternary
• Nucleic acids are viewed is the same way
– Primary structure: order of bases in
polynucleotide
– Secondary structure: 3D conformation of the
backbone
– Tertiary structure: supercoiling of the molecule

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What are nucleic acids?

• Nucleic acids are large biological molecules,
essential for all known forms of life.
• Nucleic acids, which include DNA
(deoxyribonucleic acid) and RNA (ribonucleic acid),
are made from monomers known as nucleotides
linked in a chain through phosphodiester bonds.
• In all biological systems, they serves as information-
carrying molecules or, in the case of some RNA
molecules are catalysts (e.g. ribozyme).

Deoxyribonuclei Acid (DNA)

Determines the genetics make-up of living
organisms (e.g. phenotypes)

Directs synthesis of proteins

Enables cells to reproduce or make other
copies of themselves (replication ; mitosis/
meiosis)

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What are nucleotides?

• Nucleotides are organic molecules that serve
as the monomers, or subunits, of nucleic acids
like DNA and RNA.
• The building blocks of nucleic acids
• Nucleotides are composed of
– a nitrogenous base,
Nucleosides
– a five-carbon sugar (ribose or deoxyribose),
– and at least one phosphate group.

DNA Structure

Is made up of two strands to form a double
helix structure

Each strand is made up of nucleotides

Nucleotides consists of pentose sugar - a
five-carbon sugar, ribose or deoxyribose,
nitrogenous base and phosphate

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Structure and Chemistry of

Nitrogenous Bases
• Pyrimidines
– Cytosine (DNA, RNA)
– Uracil (RNA)
– Thymine (DNA)
• Purines
– Adenine (DNA, RNA)
– Guanine (DNA, RNA)

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Purines and Pyrimidines

There are two kinds of nitrogenous bases: Purines & Pyrimidines

Purines
NH2 O

N N
N NH

N N N NH2
N

Adenine Guanine
O
Pyrimidines O
H2N NH
H3C
NH N O
N
ribose
N O Uracil
N O

Cytosine Thymine

DNA and RNA

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DNA Structure
• Nitrogenous bases – Adenine (A), Guanine (G),
Cytosine (C), Thymine (T).

A to T, by two hydrogen bonds

C to G, by three hydrogen bonds

Nucleotides are joined together by
phosphodiester bond

2 nucleotides – dinucleotides

Many - polynucleotides

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Base pairs

Non-covalent hydrogen bonds between

the pairs are shown as dashed lines.

DNA Structure

Higher GC content results in higher melting
temperatures

the genomes of extremophile organisms such
as Thermus thermophilus are particularly GC-
rich.

On the other hand, regions of a genome that
need to separate frequently — for example,
the promoter regions for often-transcribed
genes — are comparatively GC-poor.

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How does nucleotide forms nucleic acids?

• Nucleotides join together through
phosphodiester linkages between the 5' and 3'
carbon atoms to form nucleic acids.
• The 3' -OH of the sugar group forms a bond with
one of the negatively charged oxygen of the
phosphate group attached to the 5' carbon of
another sugar.
• When many of these nucleotide subunits
combine, the result is the large single-stranded
polynucleotide or nucleic acid, DNA

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Nucleic acid polymers

Polymers linked 3' to 5' by phosphodiester
bridges (Ribonucleic acid and
deoxyribonucleic acid)

Know the shorthand notations

Sequence is always read 5' to 3'
Eg: 5’-CTTAGATACGTTGCCAGG-3’

In terms of genetic information, this
corresponds to "N to C" in proteins

DNA & RNA Differences

Why is DNA 2'-deoxy and RNA is not?
• Hydroxyl (OH) groups (2' and 3') in RNA make
it more susceptible to hydrolysis
• DNA, lacking 2'-OH is more stable
• This makes sense - the genetic material must
be more stable
• RNA is designed to be used and then broken
down

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O H N N H
O
O P
12 Hist
H N N H
O O O
119 Hist

H N N H
O O
H N N P 12 Hist
O O O
H H
119 Hist

O N N H
O

H N N H 12 Hist
O
119 Hist HO O
O P OH
O
O

The Uracil base

• The uracil base replaces thymine in RNA
• Uracil has fundamentally the same structure as
thymine, with the deletion of a methyl group at the
5' position
• Uracil pairs with adenine in the same way as thymine
pairs with adenine.

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What Are the Different Classes of

Nucleic Acids?
• DNA - one type, one purpose
• RNA - 3 (or 4) types, 3 (or 4) purposes
– ribosomal RNA - the basis of structure and
function of ribosomes
– messenger RNA - carries the message
– transfer RNA - carries the amino acids

Hydrolysis of Nucleic Acids

Dilute acid Dilute base

DNA is DNA is not

depurinated by susceptible to
dilute acid base

RNA is RNA is
resistant to hydrolyzed by
dilute acid dilute base

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Functions of Nucleotides
• Nucleoside 5'-triphosphates are carriers of
energy
• Bases serve as recognition units
• Cyclic nucleotides are signal molecules and
regulators of cellular metabolism and
reproduction:
i. ATP is central to energy metabolism (cAMP)
ii. GTP drives protein synthesis (cGMP)
iii. CTP drives lipid synthesis (cCMP)
iv. UTP drives carbohydrate metabolism (cUMP)

cAMP is a derivative of adenosine

triphosphate (ATP) and used for
intracellular signal transduction in
many different organisms

Cyclic guanosine
monophosphate (cGMP) is a cyclic
nucleotide derived from guanosine
triphosphate (GTP)
cGMP acts as a second messenger much
like cyclic AMP, activation of
intracellular protein kinases

The 'cyclic' portion consists of two bonds between the phosphate group
and the 3' and 5' hydroxyl groups of the sugar, very often a ribose.

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The DNA Double Helix

• Stabilized by hydrogen bonds!
• "Base pairs" arise from hydrogen bonds
• Erwin Chargaff had the pairing data, but didn't
understand its implications
• Rosalind Franklin's X-ray fiber diffraction data
was crucial
• Francis Crick knew it was a helix
• James Watson figured out the H bonds

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Structure of DNA
• Double helix – James Watson and Francis Crick (1953)

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Antiparallel Orientation

Figure 4-4 Molecular Biology of the Cell (© Garland Science 2008)

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DNA – Antiparallel strands

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Types of RNA
Translation : rRNA, tRNA and mRNA ?
B.

A. C.

Ribonucleic Acid (RNA)

• Ribonucleic acid (RNA) is a linear molecule
composed of four types of smaller molecules
called ribonucleotide bases: adenine (A),
cytosine (C), guanine (G), and uracil (U).
• Ribose sugar (hydroxyl group, OH at 2` carbon)
• Complementary : A to U, C to G.
• A few types ; mRNA, tRNA, rRNA, miRNA,
snRNA, snoRNA, lncRNA

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Messenger RNA (mRNA)

A single-stranded molecule that is transcribed

from a DNA coding strand.

Originates in the nucleus and migrate to the
ribosome in the cytoplasm in preparation for
the process protein synthesis

Consists of a sequence of mRNA nucleotide
(several thousands).

Transfer RNA (tRNA)

Transcribed from DNA

A single strand, only about 80
nucleotides long and has a cloverleaf
shape

Function – to carry amino acids that
will be linked into the polypeptide
molecule specified by a particular
sequence of bases on the mRNA
(codon/anticodon)

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Transfer RNA (tRNA)

• Each type of tRNA carries only one of

the 20 amino acids.
• Some amino acids can be carried by
more than one tRNA molecule.
• The other end of tRNA molecule has
three nucleotides (the anticodon)
which attach to the matching set of
three nucleotides (codon) on the
mRNA molecule.

Ribosomal RNA (rRNA)

• ribosomal ribonucleic acid (rRNA) is the RNA
component of the ribosome, and is essential
for protein synthesis in all living organisms. It
constitutes the predominant material within
the ribosome, which is approximately
60% rRNA and 40% protein (ribosomal
protein) by weight.

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Ribosomal RNA (rRNA)

End of lecture

Acknowledgement:
Azani Saleh FSG UiTM Shah Alam

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