Unit 6 Nucleic Acids 23

6
Nucleic Acids
Biochemistry 22/23
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CONTENTS
1. Introduction.
2. Nucleotides.
3. Phosphodiester bond.
4. DNA.
5. RNA.
6. The flow of genetic information.
7. The genetic code.

1. INTRODUCTION
DNA and RNA are long linear polymers, called nucleic acids, that carry
information in a form that can be passed from one generation to the next.
These macromolecules consist of a large number of linked nucleotides,

each composed of a sugar, a phosphate and a base.
Sugars linked by phosphates form a common backbone that plays a

structural role, whereas the sequence of bases along a nucleic acid strand
carries genetic information.
The DNA molecule has the form of a double helix, a helical structure
consisting of two complementary nucleic acid strands.
Each strand serves as the template for the other in DNA replication.
The genes of all cells and many viruses are made of DNA.
© Copyright Universidad Europea. Todos los derechos reservados 3
1. INTRODUCTION
Base i Base i+1 Base i+2
… Sugar Sugar Sugar

Phosphate Phosphate Phosphate
There are two types of nucleic acids: deoxyribonucleic acid (DNA) and ribonucleic acid (RNA).
Constituents: C, H, O, N, P.
A nucleic acid consists of four kinds of bases linked to a sugar-phosphate backbone.
Nucleotides are the monomeric units of nucleic acids.

1. INTRODUCTION
Replication
DNA RNA Proteins
Transcription Translation

1. INTRODUCTION
Genes specify the kinds of proteins that are made by cells, but DNA is not
the direct template for protein synthesis.
Rather, a DNA strand is copied into a class of RNA called messenger RNA
(mRNA), the information-carrying intermediates in protein synthesis. This
process of transcription is followed by translation, the synthesis of protein
according to instructions given by mRNA.
Information processing in all cells is quite complex.

1. INTRODUCTION
Both DNA and RNA contain two major purine bases, adenine (A) and guanine (G), and two major
pyrimidines.
In both DNA and RNA, one of the pyrimidines is cytosine (C), but the second major pyrimidine is not
the same in both: is thymine (T) in DNA and uracil (U) in RNA.
Nucleic acids have two kinds of pentoses. The recurring deoxyribonucleotide units of DNA contain
2'-deoxy-D-ribose, and the ribonucleotides units of RNA contain D-ribose.
The functions units of these polymers are:
✓ Nitrogenous base.
✓ Base + sugar = nucleoside.
✓ Nucleoside + phosphate = nucleotide.
✓ Nucleic acid: polymers of thousands of nucleotides joined by ester bonds.

1. INTRODUCTION
Base Nucleoside Nucleotide

2. NUCLEOTIDES
Nucleotides have three characteristic components:

(1) a nitrogenous base (nitrogen-containing),
(2) a pentose,
(3) a phosphate.
Phosphoric acid Ribose Deoxyribose

2. NUCLEOTIDES
The nitrogenous bases are derivatives of two parent compounds, pyrimidine
and purine.
❑ Purine bases: adenine (A) and guanine (G).
(A) (G)
❑ Pyrimidine bases: cytosine (C), thymine (T) and uracil (U).
(C) (T) (U)

2. NUCLEOTIDES
A unit consisting of a base bonded to a sugar is referred to as a nucleoside.
The base of a nucleoside is joined covalently in an N-glycosidic bond to the pentose,
involving a N atom of the base and a C atom of the pentose.
The four nucleoside units in RNA are called adenosine, guanosine, cytidine and
uridine, whereas those in DNA are called deoxyadenosine, deoxyguanosine,
deoxycytidine and thymidine.
2. NUCLEOTIDES
A nucleotide is a nucleoside joined to one or more phosphoryl groups by an ester linkage.
Nucleotide triphosphates, nucleosides joined to three phosphoryl groups, are the monomers that
are linked to form RNA and DNA. However, the units that link to form DNA are nucleotides
monophosphates.
The four nucleotides units in DNA are called deoxyadenylate, deoxyguanylate, deoxycytidylate
and thymidylate, whereas adenylate, guanylate, cytidylate and uridylate form RNA.
2. NUCLEOTIDES
Adenine Thymine
Ribose Deoxyribose
2. NUCLEOTIDES
−H2O

2. NUCLEOTIDES
−H2O
2. NUCLEOTIDES
Nucleotide triphosphate
Nucleotide diphosphate
Nucleotide monophosphate
NH
O O O
-O P O P O P O CH2
O
N O
Nucleoside
O- O- O- C H H C
C C
H H
OH H

2. NUCLEOTIDES
PENTOSE BASE NUCLEOTIDES
Adenine AMP ADP ATP
Guanine GMP GDP GTP

Ribose
Cytosine CMP CDP CTP
Uracil UMP UDP UTP
Adenine dAMP dADP dATP
Guanine dGMP dGDP dGTP

Deoxyribose
Citosine dCMP dCDP dCTP
Thymine dTMP dTDP dTTP

2. NUCLEOTIDES
Both DNA and RNA contain two major purine bases, adenine (A) and guanine (G), and two major
pyrimidines.
In both DNA and RNA, one of the pyrimidines is cytosine (C), but the second major pyrimidine is not
the same in both: is thymine (T) in DNA and uracil (U) in RNA.
Nucleic acids have two kinds of pentoses. The recurring deoxyribonucleotide units of DNA contain
2'-deoxy-D-ribose, and the ribonucleotides units of RNA contain D-ribose.
The functions units of these polymers are:
✓ Nitrogenous base.
✓ Base + sugar = nucleoside.
✓ Nucleoside + phosphate = nucleotide.
✓ Nucleic acid: polymers of thousands of nucleotides joined by ester bonds.

2. NUCLEOTIDES
A nucleotide chain ranging from 13 to 25 units is known as an

oligonucleotide. A longer nucleic acid is called polynucleotide.
Nucleotides perform different functions in the body:
✓ They transmit hereditary characters.
✓ They transport energy.
✓ They act as coenzymes, such as in CoA.
✓ Mediators in intracellular signal transmission processes: cAMP.

2. NUCLEOTIDES
When food is oxidized or decomposes, the energy released is coupled to the conversion of
ADP to ATP.
This chemical energy will be invest later in doing biological work (chemical, electrical, osmotic
and mechanical).
ΔG of hydrolysis of the phosphoryl groups is negative (exergonic):

NH2
N
O O O
O N
P P P
O O O N
O
O O O N
HO OH
ATP + H2O  ADP + Pi + H+ (G = −30.5 kJ/mol)

ADP + H2O  AMP + Pi + H+ (G = −30.5 kJ/mol)
AMP + H2O  Adenosina + Pi + H+ (G = −14.2 kJ/mol)
2. NUCLEOTIDES
A variety of enzyme cofactors fulfill a wide range of chemical functions include adenosine as part
of their structure.
Some coenzymes containing adenosine, such as CoA (coenzima A).
Cells respond to their environment by taking cues from hormones or other external chemical
signals.
The interaction of these extracellular chemical signals (“first messengers") with receptors on the
cell surface often leads to the production of second messengers inside the cell, which in turn leads
to adaptive changes in the cell.
One of the most common second messengers is adenosine 3,5-cyclic monophosphate (cyclic
AMP, or AMPc), which fulfil regulatory functions in virtually all cells outside the plant kingdom.
Examples: vitamins B1, B2, B3, B5, B6, B12.

3. PHOSPHODIESTER BOND
The successive nucleotides of both DNA and RNA are covalently linked through
phosphate-groups “bridges” in which the 5’-phosphate group of one nucleotide unit
is joined to the 3’-hydroxyl group of the next nucleotide, creating a phosphodiester
bond.
DNA molecules have directionality. One end of the chain has a free 5'-OH group (or a
5'-OH group attached to a phosphoryl group) and the other end has a free 3'-OH
group, neither of which is linked to another nucleotide. By definition, the 5’ end lacks
a nucleotide at the 5’ position and the 3‘ end lacks a nucleotide at the 3’ position.
Between successive nucleotides there are 3’ → 5’ phosphodiester bonds, linking the

3'-OH of one nucleotide to the 5'-OH of the next.
By convention, the base sequence is written in the 5 ’ to 3’ direction.

3. PHOSPHODIESTER BOND
5’
Nucleotides
joining
3’

4. DNA
The primary structure of DNA consists of a linear sequence of nucleotides that are
linked together by phosphodiester bonds:
Constituents: deoxyribose + nitrogenous base (A, T, C, G) + phosphate

4. DNA
The DNA secondary structure is a double helix.
It is a double strand of deoxyribonucleotides, which are joined through their

nitrogenous bases (inside) by hydrogen bonds.
In all cellular DNA, regardless of the species, the number of adenosine residue is
equal to the number of thymidine residues (A = T), and the number of guanosine
residues is equal to the number of cytidine residues (G = C).
From these relationships, it is easy to deduce that the number of purine residues is
equal to the nuber of pyrimidine residues: A + G = T + C.
These quantitative relationships are called Chargaff´s rules.

4. DNA

4. ADN
Species A:T G:C A:G

Humans 1.00 1.00 1.56
Salmon 1.02 1.02 1.43
Wheat 1.00 0.97 1.22
Yeast 1.03 1.02 1.67
E. Coli 1.09 0.99 1.05

4. DNA
In 1953, Watson and Crick postulated a three-dimensional model of DNA structure
that accoiunted for all the available experimental data.
It consist in two helical DNA chains wound around the same axis to form a right-
handed double helix. The strands are antiparallel, meaning that they have opposite
directionality.
The hydrophilic backbone of alternating deoxyribose and phosphate groups are on

the outside of the double helix, facing the surrounding water.
The offset pairing of two strands create a major groove and minor groove on the
surface of the duplex where proteins and drugs may bind.
The Watson-Crick structure is also referred to as B-form, or DNA-B. The B form is the
most stable structure for a random-sequence DNA molecule under physiological
conditions.
4. DNA
3’ 5’
5’ 3’
The pentose-phosphate axes of the chains are located
peripherally, like the handrail of a spiral staircase.
The bases are arranged perpendicularly inwards, like the rungs of a ladder.
4. DNA

4. DNA
Inside the helix, the bases are essentially stacked one on top of another.
The stacking of base pair contributes to the stability of the double helix in two ways.
✓ First, the formation of the double helix is facilitated by the hydrophobic effect. The
hydrophobic bases cluster in the interior of the helix away from surrounding water,
whereas the more polar surfaces are exposed to water. This arrangement is
reminiscent of protein folding, where hydrophobic amino acids are in the protein´s
interior and the hydrophilic amino acids are on the exterior.
✓ Second, the stacked base pairs attract one another through van der Waals forces,
appropriately referred to as stacking forces, futher contributing to stabilization of
the helix.

4. DNA
The cornerstone of the stability of the double helix is hydrogen bonding.
Guanine can be paired with cytosine and adenine with thymine to form base pairs
that have essentially the same shape.
These base pairs stabilize the helix because of their large numbers in a DNA molecule.
A-T G-C
As between C and G there are 3 hydrogen bonds, and between A and T there are 2, it
will be easier to separate the two DNA strands (split them using heat) if there are more
A-T pairs than C-G, since fewer hydrogen bonds must be broken.
5.RNA
RNA is similar to DNA, although it has some differences:
✓ RNA ´s sugar is the ribose and among its nitrogenous base uracil is
present instead of thymine of DNA.
✓ RNA is usually single stranded, so the secondary structure is a simple

helix.
✓ RNA contains U and not T.

5.RNA
Unlike DNA, most RNAs carry out their functions as single strands, which fold back on
themselves and have a potential for much greater structural diversity than DNA.
5.RNA
Scientists used to believe that RNA played a passive role in gene expression, as a
mere information carrier. However, recent investigations have demonstrated that
RNA plays a variety of roles, from catalysis to regulation.
Cells contain several kinds of RNA:
✓ Messenger RNA (mRNa) is the template for protein synthesis or translation.
✓ Transfer RNA (tRNA) carries amino acids in an activated form to the ribosome for
peptide-bond formation, in a sequence dictated by the mRNA template.
✓ Ribosomal RNA (rRNA) is the major component of ribosomes. It is the actual

catalyst for protein synthesis.

5.RNA
Differences DNA RNA
Sugar Deoxyribose Ribose
Less stable due to OH

Reactivity More stable
of ribose (hydrolysis)
Nitrogenous base Contain thymine Contain uracil
Structure Double helix Single helix
Heredity, evolution,
Function reproduction, protein Protein synthesis
synthesis
Nucleus, mitochondria, Nucleolus, cytoplasm,

Location
chloroplasts ribosomes

6. THE FLOW OF GENETIC INFORMATION
The fundamental unit of information in living systems is the gene. A gene can be defined
biochemically as a DNA segment (or, in a few cases, RNA) that encodes the information
required to produce a functional biological product. The final product is usually a protein.
The central dogma of molecular biology comprises the three major processes in the cellular use
of genetic information.
✓ The first is replication, the copying of parental DNA to form daughter DNA molecules with
identical nucleotide sequences.
✓ The second is transcription, the process by which parts of the genetic message encoded in
DNA are copied precisely into RNA.
✓ The third is translation, whereby the genetic message encoded in messenger RNA is
translated on the ribosomes into a polypeptide with a particular sequence of aminoacids.

Replication
DNa RNA Proteins
Transcription Translation

The transcription process is analogous to copying, word to word, a book page. There
is no change of alphabet or vocabulary; so the likelihood of a change in meaning is
small.
Translating the base sequence of an mRNA molecule into a sequence of amino

acids is analogous to translating the book page into another language.
DNA and RNA molecules are written in a language of four nucleotides; meanwhile,
the protein language includes 20 amino acids. Codons (sequences of three
nucleotides) provide the key that allows these two languages to be translated into
each other.
Translation is a complex process, which involves many steps and dozens of

molecules. The potential error exists at each step.
7. THE GENETIC CODE
The genetic code is the relation between the DNA bases sequence (or its RNA
transcripts) and the amino acids sequence in proteins.
DNA Proteins
(information) (function)
Nucleotides Amino acids

polymer polymer
Genetic code
40
7. THE GENETIC CODE
The main features of the genetic code are:
✓ An amino acid is encoded by a group of three bases, or codon.
✓ The code is nonoverlapping: considering a base sequence ABCDEF, ABC

designates the first amino acid, DEF the second, etc. (instead of ABC, BCD, CDE
...).
✓ The sequence of bases is read sequentially from a fixed starting point, whitout
punctuation (there is not one base which serve as a “comma” between groups of
three bases).
✓ The code has directionality: it can read from 5 ‘ end of the messenger RNA to its
3’ end.

7. THE GENETIC CODE
The main features of the genetic code are:
✓ The genetic is degenerate: most amino acids are encoded by more than one codon; there are 43 =
64 possible base triplets and only 20 amino acids, and in fact 61 of the 64 possible triplets specify
particular amino acids. Thus, for most amino acids, there is more than one keyword.
✓ Since most synonyms differ only in the last base of the triplet, degeneracy minimizes the deleterious
effects of mutations.
✓ Three triplets (called stop codons) designate the termination of translation.
✓ AUG is part of the initiation signal of translation, in addition to coding for internal methionine residues.

7. THE GENETIC CODE
The complete set of relationship between codons and amino acids (or stop
signals) is known as the genetic code. Frequently, genetic code is summarized as a
table:

Alison Plowden
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These macromolecules consist of a large number of linked nucleotides,

Sugars linked by phosphates form a common backbone that plays a

Base i Base i+1 Base i+2

… Sugar Sugar Sugar

A nucleic acid consists of four kinds of bases linked to a sugar-phosphate backbone.

Nucleotides are the monomeric units of nucleic acids.

© Copyright Universidad Europea. Todos los derechos reservados 4

DNA RNA Proteins

© Copyright Universidad Europea. Todos los derechos reservados 5

Information processing in all cells is quite complex.

© Copyright Universidad Europea. Todos los derechos reservados 6

The functions units of these polymers are:

✓ Base + sugar = nucleoside.

✓ Nucleoside + phosphate = nucleotide.

✓ Nucleic acid: polymers of thousands of nucleotides joined by ester bonds.

Base Nucleoside Nucleotide

Nucleotides have three characteristic components:

Phosphoric acid Ribose Deoxyribose

❑ Pyrimidine bases: cytosine (C), thymine (T) and uracil (U).

(C) (T) (U)

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PENTOSE BASE NUCLEOTIDES

Adenine AMP ADP ATP

Guanine GMP GDP GTP

Guanine dGMP dGDP dGTP

Thymine dTMP dTDP dTTP

The functions units of these polymers are:

✓ Base + sugar = nucleoside.

✓ Nucleoside + phosphate = nucleotide.

✓ Nucleic acid: polymers of thousands of nucleotides joined by ester bonds.

A nucleotide chain ranging from 13 to 25 units is known as an

Nucleotides perform different functions in the body:

✓ They transmit hereditary characters.

✓ They transport energy.

✓ They act as coenzymes, such as in CoA.

✓ Mediators in intracellular signal transmission processes: cAMP.

© Copyright Universidad Europea. Todos los derechos reservados 19

ΔG of hydrolysis of the phosphoryl groups is negative (exergonic):

ATP + H2O  ADP + Pi + H+ (G = −30.5 kJ/mol)

Some coenzymes containing adenosine, such as CoA (coenzima A).

Examples: vitamins B1, B2, B3, B5, B6, B12.

© Copyright Universidad Europea. Todos los derechos reservados 21

Between successive nucleotides there are 3’ → 5’ phosphodiester bonds, linking the

By convention, the base sequence is written in the 5 ’ to 3’ direction.

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Constituents: deoxyribose + nitrogenous base (A, T, C, G) + phosphate

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It is a double strand of deoxyribonucleotides, which are joined through their

These quantitative relationships are called Chargaff´s rules.

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Species A:T G:C A:G

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The hydrophilic backbone of alternating deoxyribose and phosphate groups are on

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✓ RNA is usually single stranded, so the secondary structure is a simple

✓ RNA contains U and not T.

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