NUCLEIC ACIDS

INTRODUCTION
The subject biochemistry is functionally divided into two major aspects
1. Biochemistry of homeostasis that is, metabolism and
2. Biochemistry of growth and production that is cellular biosynthesis.
The biochemistry of growth, reproduction or cellular biosynthesis centers on the function of the
nucleic acids. It therefore, becomes imperative to discuss the properties as well as the
components structure of nucleic acids in order to better appreciate these functions.
Nucleic acids could be defined as naturally occurring compounds that are capable of being
hydrolysed to produce sugars, phosphoric acid, and a combination of purines and pyrimidines as
organic bases.

Generally, nucleic acids are better defined as acidic chainlike biological macromolecules which
constitute multiple units of nucleotides with each nucleotide unit consisting of a nitrogenous
(nitrogen-containing) base, pentose sugar and phosphoric acid. These nucleic acids (monomers
of nucleotides) are important for a number of reasons. Most nucleic acid, not just ATP, are the
sources of energy that drive most of our reactions. ATP is the most commonly used source but
GTP is used in protein synthesis as well as a few other reactions. UTP is the source of energy
which is necessary for activating glucose and galactose. CTP is another energy source in lipid
metabolism. AMP is part of the structure of some of the coenzymes like NAD and Coenzyme A.
Neither the nucleotides nor the bases are required dietary components. We can both synthesize
them de novo and salvage and recycle those we already have.
Nucleic acids—the primary information-carrying molecules of the cell—determine the inherited
traits of every living creature. Deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) are the
two primary types of nucleic acids. All free-living organisms and the majority of viruses have
genetic material made up of DNA, which is the ultimate life-plan. RNA is the genetic material of
some viruses, but it is also present in all living cells and is crucial to many biological activities,
including the synthesis of proteins.

Learning Outcome
After you have studied this study session, you should be able to:

Define nucleic acids.

State the types of nucleic acids.
Discuss the hydrolysis of nucleic acid
 State the components of nucleic acids
State the function of each type of nucleic acid.
State the components of nucleic acids
Explain how nucleotides are joined together to produces nucleic acids.
Explain the DNA secondary structure and the importance of complementary base pairing.
Explain why certain nucleotides are present in DNA but not RNA and vice versa.
Mention other nucleotides not seen in nucleic acids
What histones are
Identify structural differences between RNA and DNA.
State the different types of RNA and their functions.
State the components of each type of RNA
Describe the various processes involved in RNA processing.

THE DISCOVERY OF NUCLEIC ACIDS

The first isolation of nucleic acid from the nuclei of pus cells was described in 1869 by a Swiss
physician Miescher. They also isolated the same substance from Salman sperm and later
demonstrated that these isolated substances consist of a basic protein called protamine and an
acid components now known as nucleic acid.

HYDROLYSIS OF NUCLEAR PROTEIN

The treatment of nuclear protein with idle detergent, acids or high salt concentrations separate
the basic protein protamine from the nucleic acid components. nucleic acids and nitrogen
containing compounds of high molecular weight found in association with proteins in the cells
and two main types are known ribonucleic acid RNA and the oxy ribonucleic acid DNA both
forms of nucleic acids are the molecular representative store for genetic information and so the
structure of proteins are hence cell constituents remain the products of information programs into
nuclear tide sequence.
Fig. 1: hydrolysis of nucleoproteins
The enzymic hydrolysis of nucleic acids by either RNAse or DNAse as the case may be, yields
mononucleosides under controlled conditions. For the hydrolysis by phosphatase gives inorganic
phosphate and nucleosides.
Nucleotidase ordinarily convert nucleoside into bases (purine/ pyrimidine) and sugars (ribose all,
or deoxyribose). Thus the complete hydrolysis of nucleic acid produces purine and pyrimidine
basis, deoxy ribose or ribos sugar and inorganic phosphate. Fig 1.
Common sources of nucleic acid used by early workers where mainly the thymus gland.
Hydrolysis of thymus nucleic acids yielded purine and pyrimidine bases, deoxyribose and
phosphates.
Other used sources produced phosphate and similar bases but ribose in lieu of deoxyribose. It
was consequently observed that thymus nucleic acid contains mostly DNA and yeast nucleic
acids mostly RNA. Nonetheless all cells contain both forms but some as above could contain
more of one type than the other.

CHEMICAL COMPOSITION OF NUCLEIC ACIDS.

Nucleic acid consists of chains of nucleotides joint together by phosphodiester bonds.
Nucleotides are the basic building blocks of nucleic acids and themselves are parcels containing
three molecules namely nitrogen base, pentose sugar and phosphate joined together. Nucleic acid
bases are heterocyclic aromatic rings, usually containing carbon and nitrogen atoms such rings
have varieties of side substituents.

Two types of bases are obviously recognized: pyrimidines which monocyclic rings containing
six atoms: two and four atoms of nitrogen and carbon respectively. The three pyrimidine bases
include cytosine(C) thymine (T) and uracil (U). The second type of nucleic acid base is purine
which is a bicycling structure with imidazole ring fused to pyrimidine base. There are two types
of purines bases found in DNA and RNA; adenine (A) and guanine (G).

COMPONENTS AND PRIMARY STRUCTURE OF NUCLEIC ACIDS

Basically, the nucleic acid is a polymer of nucleotides. A nucleotide is made up of a nitrogen
base, a sugar moiety and a phosphate group
Nitrogenous base

A nitrogenous base is an organic molecule consisting of nitrogen that is a component of nucleic

acids. The basic properties of nitrogenous bases are determined by the lone pair of electrons on
their nitrogen atoms. There are two types of nitrogenous bases: pyrimidines, which have a six-
atom monocyclic ring ( the nitrogens at positions 1 and 3 in the ring); and purines, which have a
bicyclic structure with an imidazole ring fused to a pyrimidine base, purines consist of a six-
membered and a five-membered nitrogen-containing ring fused together with nitrogens located
at positions 1, 3, 7, and 9 within the structure. Adenine and guanine are examples of purines
while cytosine, thymine, and uracil are pyrimidines. These nitrogenous bases form the building
blocks of nucleotides and DNA strands.

Fig …. (a) Structure of purine (b) Structure of pyrimidine

Purines are organic compounds that can be found in high concentrations in meat, specifically in
liver and kidney. They are found in smaller quantities in plant-based diets. Sources with high
levels of purines include sardines, sweetbreads, beer (from the yeast), kidney and liver.
Additionally, a moderate amount of purine can be found in various other food sources such as
beef, pork, poultry, seafood, vegetables, legumes, and grains. While higher levels of meat and
seafood consumption are associated with an increased risk of gout, moderate intake of purine-
rich vegetables or protein is not associated with an increased risk. Purines such as adenine and
guanine can be found in both RNA and DNA molecules. Hypoxanthine and Xanthine are
necessary intermediates in the breakdown and synthesis of the purine nucleotides, but are not
combined into the nucleic acids as they are being synthesized. The minor purine bases,
Hypoxanthine and Xanthine, are found in small amounts in nucleic acids.

Types of Purine Types of Pyrimidine

1. Adenine = 6-amino purine 1. Uracil = 2,4-dioxy pyrimidine

2. Guanine = 2-amino-6-oxy purine 2. Thymine = 2, 4-dioxy-5-methyl pyrimidine

3. Xanthine = 2, 6-dioxy purine 3. Cytosine = 2-oxy-4-amino pyrimidine

4. Hypoxanthine = 6-oxy purine 4. Orotic acid = 2, 4-dioxy-6-carboxy pyrimidine

5. Uric acid = 2, 6, 8-trioxy purine

Fig. 2.0 the different nitrogen bases of purine nucleotides.
Cytosine= 2-oxy-4-amonopyrimidine, Uracil= 2,4-dioxy-pyrimidine
Guanine= 2-amino-6-oxypurine, Adenine= 6-aminopurine and Thymine= 5-methyluracil
*DNA do not contain uracil and RNA do not contain thymine.
Note that thymine is 5-methyluracil. Exceptionally, germ DNA contains 5-methylcytosine and
the DNA of certain bacteria and viruses also have 5-hydroxymethycytosine.
It is important to mention that there are other forms of purine bases which are not normally
found in nucleic acids. Example is uric acid, the end product of purine oxidation metabolism in
man. Other examples include the intermediates of adenine and guanine degradation which
includes; inosine, hypoxanthine and xanthine. Fig 3.0

Fig. 3.0; intermediates of purine break down metabolism

In plants also, a series of purine bases containing ethyl substituents occur and many of such have
medicinal values. Example include caffein, theophylline Theobromine.

Fig. 4.0; purine bases found in plants

Pentose Sugar: Pentose Sugar is a component of Nucleic acid (nucleotide monomers) which is a
monosaccharide with five carbon atoms. The pentose sugar in RNA is D-ribose which occurs in
the furanose form; the sugar in DNA is D-2-deoxyribose.

D-ribose D-2-deoxyribose

In deoxyribose, oxygen is missing at position 2,it is a component of

deoxyribonucleic acid (DNA). The hydroxyl group attached to carbon number 1 is replaced with
nucleotide bases in nucleic acids.

NUCLEOSIDES
In nucleic acids, the bases are covalently attached to the first position of a pentose sugar ring to
form a nucleoside. A nucleoside therefore, consist of a purine or pyrimidine base bound to a
pentose sugar which is a B-D-2’-ribose (B-D-2’-ribofuranose) in RNA and B-D-2’-Deoxyribose
(B-D-2’-Deoxyribofuranose) in DNA. In B-D-2'-DEOXYRIBOSE, the oxo group at the 2'
position is replaced by hydrogen. In pyrimidines, the 1-position (N-1) is the point of attachment
whereas, it is N-9 for purine.
The nucleosides of B-D-ribose (ribonucleosides) with adenine, cytosine and uracil, respectively.
But if the sugar is B-D-2'-Deoxyribose, the resulting deoxyribonucleotide would-be
deoxyadenosine, deoxyguanosine, deoxycytosine and deoxythymidine, though, thymine and
deoxythymidine may be used interchangeably.
To distinguish the numbering on the base from the sugar Moiety, a superscript prime (') is
usually added to the number on the pentose ring. example,1',2',3' etc.
The bond between the bases and sugar is called the glycosidic (or glycosylic) bond and it is acid
labile, free rotating, theoritically occurs about this N- glycosidic Bond.
Fig. 5.0; example of nucleosides
NUCLEOTIDES
A nucleotide is a nucleoside with one or more phosphate groups covalently attached to the 3'-,5'-
or (in ribonucleosides only) the 2'- position.
If the phosphate group is esterified to the deoxyribonucleotide, the resulting compound is termed
deoxyribonucleotide.
Chemically, nucleotides are phosphate esters.
NOMENCLATURE OF NUCLEOTIDES
Conventionally, the abbreviations A, G, C, T and U could be used to designate nucleoside in vis-
a-vis the purine or pyramidine it contains. Nevertheless the prefix’d’ is usually added if the sugar
of the nucleoside is 2' deoxyribose; e.g, dA is 2'-deoxyadenosine.
The position of a phosphate in a nucleoside is indicated by an Arabic number. For instance
adenosine with the phosphate group attached to carbon five of the ribose sugar would be
adenosine-5-monophosphate, commonly abbreviated as AMP. A nucleotide of 2'
deoxyadenosine with the phosphate group bond to the carbon 5' of the sugar moiety is called 2'-
deoxyadenosine-5'-monophosphate also written as dAMP.
When two or three phosphate groups are attached to a sugar moiety DP and TP are respectively
included to the abbreviation for the corresponding purine or pyramiding nucleoside. Thus,
adenosine-5'-diphosphate and adenosine-5'-triphosphate with two and three phosphate residues
could be abbreviated as ADP and ATP respectively.
Fig. 6: Adenosine Triphosphate (ATP).
Note:
1. The nucleoside and nucleotide of thymine are synthesized with only B-D-2'-deoxyribose sugar
hence, not present in RNA.
2. The deoxyribonucleoside and deoxyribonucleotide derived from uracil actually exist but the
catalytic activity of deoxyuridine triphosphate dephosphorylase (dUTPase) hydrolyzes dUTP and
this prevents the incorporation of uracil into DNA. Since the enzyme that synthesizes DNA
(DNA polymerase III) uses deoxyribonucleoside triphosphate.
dUTP + H2O—----------->dUMP + ppi

Table 1.0: nomenclature of nucleosides and nucleotides

BASE NUCLEOSIDES NUCLEOSIDES NUCLEIC
ACID
MONO DI TRI
PRESENT
PURINE
Adenine Adenosine AMP ADP ATP RNA
2’-Deoxyadenosine dAMP dADP dATP DNA
Guanine Guanosine GMP GDP GTP RNA
 2’-Deoxyguanosine dGMP dGDP dGTP DNA
PYRIMIDINES
Cytosine Cytidine CMP CDP CTP RNA
2’-deoxycytidine dCMP dCDP dCTP DNA
Uracil Uridine UMP UDP UTP RNA
Thymine Thymidine TMP TDP TTP DNA

LINKAGES AND NUCLEOTIDE SEQUENCES IN A NUCLEIC ACID.

The successive nucleotides of both DNA and RNA are joined into a polymer by the covalent
linkage of a phosphate group or bridge. Specifically, the 5' hydroxyl group of one nucleotide unit
is linked to the 3' hydroxyl group of the next nucleotide. This kind of linkage is known as a
phosphodiester bond because the phosphate is chemically in the form of a diester.

Fig. 7; phosphodiester bond in nucleic acid

The nucleic acid backbone structure consists of alternating phosphate and pentose residues
covalently linked and the characteristics bases could be regarded as side groups (or chains)
joined to the backbone at regular intervals.
The backbone structure of both DNA and RNA are hydrophilic and the bases hydrophobic.
Linear nucleic acid molecules, no matter the length, have a free 5' end which may or may not
have any attached phosphate groups and a free 3' end most likely to be free hydroxyl groups.
Phosphate group have a single negative charge at neutrality, hence, nucleic acids are highly
charged acidic polymers.
Fig. 8; linkages and nucleotide sequence in nucleic acids

In-text question
1. Explain why uracil cannot be incorporated in DNA.
2. Why is thymidine not found in RNA?

STRUCTURE OF NUCLEIC ACIDS

The basic features of DNA structure where deduced by James Watson and Francis Crick in 1953
using the x-ray diffraction photographs of DNA fibre taken by Francis and Watson.
Based on the studies, they proposed that;

1. In DNA, two right-handed polynucleotide chains run in a helical fashion around a

common axis thus forming a double helix
2. The coiling manner is plectonemic i.e, both chains cannot be separated unless by
unwinding the coil.
3. The polynucleotide chains are antiparallel and complementary
4. The purine and pyrimidine bases of each strand are stacked in the inside of the helix with
their plane parallel to each other and perpendicular to the fibre axis (fig. 2.4).
5. The base pairs are coplanar.
6. The base pair is such that only certain base pairs fit inside the helical structure with a
diameter of 2NM. A pears with T through 2 precisely formed hydrogen bonds and G
pairs with C through three of such bonds. Therefore, purine pairs with pyrimidine and
vice versa. Purine to purine base pair (A-G) would rather be too large to fit inside the
helical [Link] the contrary pyrimidine to pyrimidine base pair e.g, C-T would
appear to be too far apart between the two NM distance to form stable hydrogen bonds.
 The allowed A-T and G-C pairs and not only of the same size but are also more strongly
hydrogen bonded than A-G and T-C pairs.
7. The relatively hydrophobic bases are within the helix shielded from water. While the
polar (hydrophilic) sugar residues and the negatively-charged phosphate groups are at the
periphery exposed to water.
8. DNA strands are stabilized by
(a) Hydrogen bonds.
(b) Hydrophobic interactions of the stacked base and
(c) Van der Waal forces.
9. The bases are stacked at a centre to centre distance of 0.34 NM termed rise per base pair
and since there are exactly 10 nucleotides residues in each complete turn i e, a secondary
repeat distance of 3.4 NM, it follows that a base pair is related to its neighbours in a
relational angle of 36°.

Fig. 9; simplified structure of DNA double helix

It is important to highlight here that much more structural variabilities of DNA have been
revealed based on x-ray analysis of DNA sequences, that today, this proposed model of Watson
and Crick is commonly regarded as a historical landmark.
The x-ray analysis of crystallized DNA deduced with definite base sequences by Richard
Dickerson and co-workers showed some local deviation from Watson and Crick findings;
1. The rotational angle between paired bases is not 36° but ranges from 28° to 42° and the
number of nucleotides pattern is about 10.5
2. DNA paired bases are not perfectly coplanar but are twisted to each other like the blades
of a propeller.
This propeller twisting properly, enhances the stacking of bases in each strands
 3. Paired bases and not parallel to their immediate neighbors but are tilted 1° away
Note: that when the relative humidity of B-DNA, the type normally found or isolated from cells
is dehydrated to below 75%, it changes to the A-form.
A-DNA like the B-DNA is a right-handed double helix with anti-parallel strands held together by
Watson and Crick base pair nonetheless both forms are illustrated below.

Table 2; structural difference between A and B-form DNA

S/N DESCRIPTION A-FORM B-FORM

1 Shape Broad Intermediate

2 Rise per base pair 0.26NM 0.24NM

3 Helix diameter 2.55NM 2.37NM

4 Tilt of base pair from normal 19° 1°

to helical axis

5 Minor grove Decreased and deep Wide and deep

6 Major grove Normal and shallow Narrow and deep

These structural differences arise from the puckering of the deoxyribose unit. In A-DNA c3 is
puckered whereas in B-DNA, c2 is puckered.

NB- number of base pairs= Total length/rise per BP.

CHARGAFF'S RULE:
1. The sum of purine bases equal the sum of pyrimidine bases. Ie, A+G=T+C
2. Adenine is equivalent to thymine and guanine is equivalent to cytosine. ie, A=T, G=C

Biochemical Properties of DNA

Denaturation
The strands of the DNA double helix are held together by hydrogen bonds. An interactions
between the complementary base pairs.
 Heating DNA in solution easily breaks these hydrogen bonds, allowing the two strands to
separate—a process called denaturation or melting.
 The two strands may re-associate when the solution cools, reforming the starting DNA
duplex—a process called renaturation or hybridization.
These processes form the basis of many important techniques for manipulating DNA.
For example, a short piece of DNA called an oligonucleotide can be used to test whether a very
long DNA sequence has the complementary sequence of the oligonucleotide embedded within it.
Using hybridization, a single-stranded DNA molecule can capture complementary sequences
from any source. Single strands from RNA can also associate. DNA and RNA single strands can
form hybrid molecules that are even more stable than double-stranded DNA. These molecules
form the basis of a technique that is used to purify and characterize messenger RNA (mRNA)
molecules corresponding to single genes.
Ultraviolet absorption
DNA melting and re-association can be monitored by measuring the absorption of ultraviolet
(UV) light at a wavelength of 260 nanometres (billionths of a metre).
 When DNA is in a double-stranded conformation, absorption is fairly weak, but when
DNA is single-stranded, the unstacking of the bases leads to an enhancement of
absorption called hyperchromicity.
Therefore, the extent to which DNA is single-stranded or double-stranded can be determined by
monitoring UV absorption
Chemical modification
After a DNA molecule has been assembled, it may be chemically modified—sometimes
deliberately by special enzymes called DNA methyltransferases and sometimes accidentally by
oxidation, ionizing radiation, or the action of chemical carcinogens. DNA can also be cleaved
and degraded by enzymes called nucleases.
Methylation
Natural methylation has many cellular functions. In bacteria and archaea, methylation forms an
essential part of the immune system by protecting DNA molecules from fragmentation by
restriction endonucleases.
In some organisms, methylation helps to eliminate incorrect base sequences introduced during
DNA [Link] marking the parental strand with a methyl group, a cellular mechanism
known as the mismatch repair system distinguishes between the newly replicated strand where
the errors occur and the correct sequence on the template strand.
In higher eukaryotes, 5-methylcytosine controls many cellular phenomena by preventing DNA
transcription. Methylation is also believed to signal imprinting, a process whereby some genes
inherited from one parent are selectively inactivated. Correct methylation may also repress or
activate key genes that control embryonic development.
On the other hand, 5-methylcytosine is potentially mutagenic because thymine produced during
the methylation process converts C: G pairs to T:A pairs. In mammals, methylation takes place
selectively within the dinucleotide sequence CG—a rare sequence, presumably because it has
been lost by mutation. In many cancers, mutations are found in key genes at CG dinucleotides.
Nucleases
Nucleases are enzymes that hydrolytically cleave the phosphodiester backbone of DNA.
Endonucleases cleave in the middle of chains, while exonucleases operate selectively by
degrading from the end of the chain. Nucleases that act on both single- and double-stranded
DNA are [Link] endonucleases are a special class that recognize and cleave specific
sequences in DNA. Type II restriction endonucleases always cleave at or near their recognition
sites. They produce small, well-defined fragments of DNA that help to characterize genes and
genomes and that produce recombinant DNAs. Fragments of DNA produced by restriction
endonucleases can be moved from one organism to another. In this way it has been possible to
express proteins such as human insulin in bacteria.

Supercoiling
Circular DNA molecules such as those found in plasmids or bacterial chromosomes can adopt
many different topologies. One is active supercoiling, which involves the cleavage of one DNA
strand, its winding one or more turns around the complementary strand, and then the resealing of
the molecule. Each complete rotation leads to the introduction of one supercoiled turn in the
DNA, a process that can continue until the DNA is fully wound and collapses on itself in a tight
ball. Reversal is also possible. Special enzymes called gyrases and topoisomerases catalyze the
winding and relaxation of supercoiled DNA. In the linear chromosomes of eukaryotes, the DNA
is usually tightly constrained at various points by proteins, allowing the intervening stretches to
be supercoiled. This property is partially responsible for the great compaction of DNA that is
necessary to fit it within the confines of the cell. The DNA in one human cell would have an
extended length of between two and three meters, but it is packed very tightly so that it can fit
within a human cell nucleus that is 10 micrometres in diameter.

Mutation
A gene mutation is a permanent alteration in the DNA sequence of a gene. Mutations can affect
one or more nucleotides (the building blocks of DNA) and can lead to changes in the protein or
RNA product that the gene encodes. Gene mutations can be caused by various factors, and they
can have a wide range of effects, both beneficial and detrimental. Anions such as bisulfite can
deaminate cytosine to form uracil, changing the genetic message by causing C-to-T transitions.
Exposure to acid causes the loss of purine residues, though specific enzymes exist in cells to
repair these lesions. Exposure to UV light can cause adjacent pyrimidines to dimerize, while
oxidative damage from free radicals or strong oxidizing agents can cause a variety of lesions that
are mutagenic if not repaired. Halogens such as chlorine and bromine react directly with uracil,
adenine, and guanine, giving substituted bases that are often mutagenic. Similarly, nitrous acid
reacts with primary amine groups—for example, converting adenosine into inosine—which then
leads to changes in base pairing and mutation. Many chemical mutagens, such as chlorinated
hydrocarbons and nitrites, owe their toxicity to the production of halides and nitrous acid during
their metabolism in the body.

Types of Gene Mutations

Point Mutations: These are changes in a single nucleotide within a gene. Point mutations can be
further classified into:
Substitution: One nucleotide is replaced by another, leading to a change in a single amino acid
in the protein.
Fig. 10: types of gene mutation
Insertion: An extra nucleotide is added to the sequence, which can shift the reading frame and
lead to significant changes in the protein.
Deletion: A nucleotide is removed from the sequence, which can also result in a shift in the
reading frame and major changes in the protein.
Frame-shift Mutations: These mutations, caused by insertions or deletions, shift the reading
frame of the gene, altering the entire amino acid sequence beyond the mutation site.
Silent Mutations: These mutations do not change the amino acid sequence of the protein, often
occurring in the third position of a codon (the "wobble" position).
Nonsense Mutations: These mutations introduce a premature stop codon, resulting in a
truncated, nonfunctional protein.
Missense Mutations: These mutations lead to the substitution of one amino acid for another in
the protein, which can affect its structure and function.
Non-coding Mutations: Mutations can occur in non-coding regions, such as introns and
regulatory sequences. These can impact gene expression and regulation.

Causes of Gene Mutations:

Spontaneous Mutations: These arise naturally during DNA replication or repair processes due
to errors made by DNA polymerases or other enzymes.
Induced Mutations: These are caused by external factors, including:
ChemicalMutagens: Substances like certain chemicals and drugs can cause mutations.
Examples include tobacco smoke and some chemotherapy agents.
Radiation: Ionizing radiation (e.g., X-rays and gamma rays) and UV radiation can induce
mutations.
Biological Mutagens: Some biological agents, like viruses, can integrate their genetic material
into the host genome, potentially causing mutations.

Effects of Gene Mutations:

Mutations can have various effects, depending on their location, type, and the protein involved.
Beneficial Mutations: Rarely, mutations can provide an advantage, such as increased resistance
to disease or environmental changes.
Harmful Mutations: Many mutations are detrimental and can lead to genetic disorders or
diseases. Examples include sickle cell anemia and cystic fibrosis.
Neutral Mutations: Some mutations have no discernible effect on an organism's phenotype and
may persist in a population without significant consequences.
Role of Mutations in Evolution:
Mutations are a source of genetic diversity in populations and provide the raw material for
natural selection and evolution.
Genetic Testing and Diagnosis:
The identification of specific mutations is essential in medical genetics and diagnostics. Genetic
testing can help diagnose genetic diseases and determine an individual's risk of developing
certain conditions.

HISTONES
Histones are essential proteins found in the cell nuclei of eukaryotes, They play a pivotal role in
the organization and regulation of DNA. They are small, positively charged proteins which
associate with DNA to form a structure called chromatin, which is critical for the packaging and
functioning of genetic material. Histones have gained significant attention in the field of
molecular biology and genetics due to their fundamental roles in gene expression, genome
stability, and epigenetic modifications.
DNA is wound round histones to form a nucleosome. Chromatin is a long collection of
nucleosomes (DNA and proteins). The chromatin condenses to form the chromosome.

Fig. 10; Nucleosome

There are five main types of histones: H1, H2A, H2B, H3, and H4 (fig. 10), each with distinct
roles in chromatin structure and function. H1 histones are involved in the compaction of
chromatin into higher-order structures, while H2A, H2B, H3, and H4 form the histone core
around which DNA wraps. This core histone octamer is a fundamental unit of chromatin and acts
as a scaffold for DNA.

One of the most well-known functions of histones is their involvement in gene regulation
through the modification of histone tails. Acetylation, methylation, phosphorylation, and other
post-translational modifications of histone tails can alter the accessibility of DNA to transcription
factors and RNA polymerase, thereby influencing gene expression. For instance, acetylation of
histone tails typically leads to a more relaxed chromatin structure, allowing for gene activation,
while methylation can have varying effects depending on the specific histone and site modified.

Histones also play a crucial role in genome stability by aiding in DNA repair and replication.
They help maintain the integrity of the genetic material and ensure accurate transmission of
genetic information during cell division. Hence, histones are central players in epigenetic
processes, which involve heritable changes in gene expression without alterations to the DNA
sequence itself. Epigenetic modifications, such as DNA methylation and histone modifications,
can influence an organism's phenotype and play a role in development, aging, and disease.

RIBONUCLEIC ACID (RNA) INTRODUCTION

The four nucleotides A, C, G, and U are connected by a backbone of alternating phosphate and
ribose sugar residues to form RNA, a single-stranded nucleic acid polymer. It is the initial step in
translating DNA information into proteins that are necessary for a cell to function. Some RNAs
have direct functions in cellular metabolism as well. A fragment of single-stranded nucleic acid
is used to replicate the base sequence of a gene, a portion of double-stranded DNA. This process,
called transcription (see below RNA metabolism), is catalyzed by an enzyme called RNA
polymerase.
Fig. 11; Transcription
Source; socratic

CHEMICAL STRUCTURE OF RNA

RNA is sensitive to oxidizing substances like periodate that cause the 3′-terminal ribose ring to
open. Because the presence of alkali causes the phosphodiester bond connecting the ribose and
phosphate groups to rapidly cleave, the 2′-hydroxyl group on the ribose ring is a major
contributor to the instability of RNA.
Since RNA is generally constantly being generated and destroyed, the instability does not pose a
serious threat to the cell.
In DNA and RNA, the interactions between the nitrogen-containing nucleotides are different.
The bases in one strand of DNA, which is often double-stranded, pair with complimentary bases
in the other strand. The bases pair with other bases inside the same molecule to form intricate
three-dimensional structures in RNA, which is typically single-stranded. Intermolecular
RNA/RNA duplexes do occasionally exist, however they take the form of a right-handed A-type
helix as opposed to a B-type DNA helix. Each turn of the helix contains either 11 or 12 base
pairs, depending on the amount of salt present.
A-type conformation is adopted by the helices that form between RNA and DNA molecules,
which are more stable than either RNA/RNA or DNA/DNA duplexes. Such hybrid duplexes are
significant species in biology because they result from the transcription of DNA into mRNA for
protein synthesis by RNA polymerase and the replication of viral RNA genomes like the human
immunodeficiency virus (HIV) by reverse transcriptase.
Single-stranded RNAs are adaptable molecules that can take many different shapes through
additional non-base pair interactions in addition to internal base pairing.
They can create longer-range connections involving the bases and phosphate residues of two or
more nucleotides, as well as hairpin loops like those in transfer RNA (tRNA). This results in
three-dimensional structures that are compact. Since there aren't many crystallographic pictures
of RNA molecules, the majority of these structures have been inferred from biochemical data.
After the RNA is transcribed, a significant number of nucleotides are changed in various forms
of RNA. Over 90 distinct changes, including several methylations and a wide range of
replacements all around the ring, have been recorded. These alterations can sometimes affect
structure and are necessary for function.
TYPES OF RNA
Messenger RNA (mRNA)
Messenger RNA (mRNA) transports the DNA-encoded data from one or more genes to the
ribosome, a specific organelle where the data is processed into a protein. Prokaryotic mRNAs
have a terminal 5′-triphosphate group and a 3′-hydroxyl residue that are a precise transcription of
the original DNA sequence. The mRNA molecules in eukaryotes are more complex. A structure
known as a cap is created by additional esterification of the 5′-triphosphate residue. Eukaryotic
mRNAs frequently have lengthy lines of adenosine residues (polyA) at the 3′ ends that are not
encoded in the DNA but are instead inserted enzymatically following transcription. Small
fragments of the original gene are typically found in eukaryotic mRNA molecules, which are
produced through a process of cleavage and rejoining from a pre-mRNA which is the initial
precursor RNA molecule and is a perfect copy of the gene (see Splicing for further information).
Prokaryotic mRNAs typically decay relatively quickly, whereas eukaryotic mRNAs include a
cap structure and a polyA tail that significantly increase their stability.

Fig. 12: DNA VS RNA

Ribosomal RNA (rRNA)

The ribosome's structural elements are called ribosomal RNA (rRNA) molecules. The vast
secondary structures that the rRNAs create help them to recognize conserved mRNA and tRNA
sequences. Additionally, they aid in the catalysis of protein synthesis. The prokaryote E. coli
produces approximately 15,000 ribosomes per cell using seven copies of the rRNA genes. The
numbers are substantially higher in eukaryotes. A single cell may have as many as 10 million
ribosomes and as many as 50 to 5,000 sets of rRNA genes. These rRNA genes loop out from the
primary chromosomal fibers in eukaryotes, where they come together to form an organelle
known as the nucleolus in the presence of proteins. The early rRNA genes are transcribed in the
nucleolus, as well as assembly of ribosomes.
Transfer RNA (tRNA).
Individual amino acids are transported by transfer RNA (tRNA) into the ribosome where they are
assembled to form the expanding polypeptide chain. The tRNA molecules are between 70 and 80.
Each of the 20 amino acids required for protein synthesis has a specialized tRNA, and many times
there are many tRNAs for each amino acid. Each three-base sequence (referred to as a codon) is
translated with a particular protein to create the protein sequence, which then becomes the
nucleotide sequence. Many less than 61 different tRNAs can read the 61 codons that are utilized
to code for amino acids (as explained in the section Translation). The 61 codons in E. coli are
translated using a total of 40 distinct tRNAs. Specialized enzymes termed aminoacyl tRNA
synthetases, typically one for each amino acid, load the amino acids onto the tRNAs. nucleotides
long and have a distinctive cloverleaf fold.
Proteins are synthesized through the translation of codons, or three-base sequences, with the help
of transfer RNA (tRNA) molecules. Each of the 20 amino acids in protein synthesis has a
specialized tRNA that is loaded with the required amino acid by aminoacyl tRNA synthetases.
The tRNA molecules are between 70 and 80 nucleotides long and have a unique cloverleaf shape.
Although there are 61 codons in E. coli, only 40 tRNAs are required to translate them, with many
tRNAs available for each amino acid (as explained in the Translation process). This process
ensures that the protein sequence is correctly built, forming the expanding polypeptide chain.

Fig. 12: tRNA

However, because some amino acids, like glutamine and asparagine, can be produced on their
respective tRNAs, not all organisms need the complete complement of 20 synthetases. Because
they all have to interact with the same locations on the ribosome, all tRNAs acquire comparable
structures.
Ribozymes
Not all cellular catalysis is performed only by proteins. Thomas Cech and Sidney Altman, who
shared the 1989 Nobel Prize, found that specific RNAs, now referred to as ribozymes, exhibited
enzymatic activity. Cech demonstrated how a noncoding segment (intron) in the protozoan small
subunit rRNA can extract itself from a much longer precursor RNA molecule and reunite the two
ends in an autocatalytic reaction. This noncoding sequence had to be excised before the rRNA
was functional. Altman demonstrated that ribonuclease P, an RNA protein complex, may cleave
a precursor tRNA to produce a mature tRNA. In addition to artificial RNAs that exhibit a range
of catalytic properties, self-splicing RNAs like the one Cech discovered also exist. It is now
largely accepted that at one point in evolution, only RNA was capable of catalyzing and storing
genetic information. This time frame, commonly referred to as "the RNA world," is thought to
have existed before DNA served as genetic material.

Antisense RNAs
The majority of antisense RNAs are synthetically altered, potentially useful variants of RNA or
DNA. The complement of the typical coding sequences found in mRNAs (also known as sense
RNAs) is present in antisense RNAs in nature. Antisense RNAs are single-stranded like mRNAs,
but they are unable to be translated into proteins. By producing a double-stranded structure that
prevents the translation of the base sequence, they can inactivate their corresponding mRNA. By
interfering with normal RNA metabolism, antisense RNAs introduced artificially into cells
selectively inactivate genes.
Viral genomes
RNA is a common genetic material for viruses. Although a few prokaryotic RNA viruses are also
discovered, eukaryotic viruses are more likely to exhibit this. The poliovirus, HIV, and influenza
viruses, which all harm people, and the tobacco mosaic virus, which infects plants, are a few
such examples. Some viruses encode their whole genetic code in a single RNA molecule,
although segmented RNA viruses may contain several RNA molecules. Reverse transcriptase is
a specialized enzyme that is used by many RNA viruses, including HIV, to allow reproduction of
the virus through a DNA intermediary. The virus can then exist in a dormant form and
successfully avoid the host immune system when this DNA intermediate integrates into the host
chromosome after infection.
Other RNAs
Cells also contain a large number of other tiny RNA molecules with unique roles. Small RNAs
that are components of the enzymes telomerase or ribonuclease P, for instance, or small nuclear
RNAs (snRNAs) that are involved in RNA splicing are components of ribonucleoprotein
particles. Other RNA molecules act as editing guides or complement tiny segments of rRNA,
directing where methyl groups should be inserted or designating U residues to be converted to
the isomer pseudouridine..
RNA PROCESSING
Cleavage
Most RNA molecules undergo processing after being created by transcription before taking on
their final form. Numerous rRNA molecules can be methylation or enzymatically changed and
are frequently cleaved from much bigger transcripts. Additionally, tRNAs frequently have extra
residues added to their 3′ end to form the sequence CCA. This is because tRNAs are typically
produced as larger precursor molecules that are cleaved by ribonuclease P to produce the mature
5′ end. The amino acid acceptor required for the function of RNA in protein synthesis is the
hydroxyl group on the ribose ring of the terminal A of the 3′-CCA sequence.
Splicing
In prokaryotes, the DNA segment containing the protein-coding sequence is one continuous
linear segment. However, Richard J. Roberts and Phillip A. Sharp independently discovered in
the 1970s that the coding sequences in eukaryotic genes are frequently "split" throughout the
genome. For their findings, they were awarded the Nobel Prize in 1993. Exons are the portions
of DNA or RNA that code for proteins, whereas introns are the non-coding sections that exist
between exons.

These coding sequences need to be combined after transcription before the mRNAs are able to
function. RNA splicing refers to the procedure of intron removal followed by exon reconnection.
A complex piece of enzyme equipment known as a spliceosome removes each intron in a unique
chain of events. Small nuclear ribonucleoprotein particles (snRNPs) that carry small nuclear
RNAs (snRNAs) make up this mechanism.
INTRONS VS EXONS
Exons:contain the actual genetic information coding for the required protein.
Introns: do not code for protein, but are important in regulation of gene [Link] are
intervening sequences and stay in the nucleus, whereas exons exit and are expressed.
Different exons are frequently combined by alternative splicing to produce a larger number of
unique [Link] splicing can produce a variety of protein products from a single
hnRNA (heterogenous nuclear RNA) sequence (eg, transmembranevs secreted Ig, tropomyosin
variants in muscle, dopamine receptors in the brain, host defense evasion by tumor cells).

Fig. ; Alternative splicing.

RNA editing
After their initial synthesis, some RNA molecules, especially those in protozoan mitochondria,
go through significant editing. Under the control of guide RNAs, a posttranscriptional
mechanism adds or deletes residues throughout this editing process. Instead of being directly
coded in the genome, this editing process may sometimes result in as much as 40% of the final
RNA molecule. Although these seem to be far more constrained in scope, several instances of
editing have also been discovered in mRNA molecules.

Self-Assessment Questions
Now that you have completed this study session you can assess how well you have achieved the
learning outcomes by answering the following questions. Write the answers in your jotter and
discuss them with your facilitator in your next study meeting.

State the function of each type.

State the components of nucleic acids
Describe how nucleotides are linked together to form nucleic acids.
Describe the secondary structure of DNA and the importance of complementary base pairing.
Explain why certain nucleotides are present in DNA but not RNA and vice versa.
Identify structural difference between RNA and DNA
State the different types of RNA and their functions.
State the components of each type of RNA
Describe the various processes involved in RNA processing.

Purine Synthesis:

Purines are synthesized as nucleotides attached to ribose 5-phosphate, with PRPP synthetase
producing PRPP as a key regulatory step. The first committed step to purine synthesis involves
the reaction of PRPP, glutamine, and water to 5'-phosphoribosylamine, glutamate, and
pyrophosphate catalyzed by pyrophosphate amidotransferase. This is not the committed step, but
is instead the committed step to pyrimidine synthesis and salvage pathways. Pyrophosphate
amidotransferase is activated by PRPP and inhibited by AMP, GMP, and IMP.

Adenine and guanine are both derived from the nucleotide inosine monophosphate (IMP), this is
the first compound in the pathway to have a completely formed purine ring system.

Inosine monophosphate is made on a pre-existing ribose-phosphate through a complex pathway

(as shown in the figure on the right). The source of the carbon and nitrogen atoms of the purine
ring, 5 and 4 respectively, come from multiple sources. Glycine contributes all its carbon (2) and
nitrogen (1) atoms, with additional nitrogen atoms from glutamine (2) and aspartic acid (1), and
additional carbon atoms from formyl groups (2), which are transferred from the coenzyme
tetrahydrofolate as 10-formyltetrahydrofolate, and a carbon atom from bicarbonate (1). Formyl
groups build carbon-2 and carbon-8 in the purine ring system, which are the ones acting as
bridges between two nitrogen atoms

.
Reactions of Purine Synthesis

5.1.1 Regulation of Purine Synthesis:

Purine biosynthesis is regulated by feedback inhibition in a manner similar to the regulation of

amino acid biosynthesis. Purine nucleotides synthesis is controlled by feedback inhibition at
several sites. Feedback inhibition of purine controls both the overall rate of purine biosynthesis
and the balance between AMP and GMP production.

• The conversion of PRPP into phosphoribosylamine by glutamine phosphoribosyl

amidotransferase. is the committed step in purine nucleotide biosynthesis. This enzyme
is feedback-inhibited by many purine ribonucleotides. It is noteworthy that AMP and
 GMP which are the final products of the pathway, are synergistic in inhibiting the
amidotransferase.

• Inosinate is the branch point in the synthesis of AMP and GMP. The reactions leading
away from inosinate are sites of feedback inhibition. AMP inhibits the conversion of
inosinate into adenylosuccinate. Likewise, GMP inhibits the conversion of inosinate into
xanthylate.

• GTP is a substrate in the synthesis of AMP and ATP is a substrate in the synthesis of
GMP. This reciprocal substrate relation tends to balance the synthesis of both adenine
and guanine ribonucleotides.

The reduction of ribonucleotides to deoxyribonucleotides is precisely controlled by allosteric

interactions. Each polypeptide of the R1 subunit of the aerobic E. coli ribonucleotide reductase
contains two allosteric sites: one of them controls the overall activity of the enzyme, whereas the
other regulates substrate specificity. The overall catalytic activity of the enzyme ribonucleotide
reductase is reduced by the binding of dATP, which signals an abundance of
deoxyribonucleotides. The binding of ATP reverses this feedback inhibition. The binding of
dATP or ATP to the substrate-specificity control sites enhances the reduction of UDP and CDP,
the pyrimidine nucleotides. The binding of thymidine triphosphate (TTP) causes the reduction of
GDP and stops the further reduction of pyrimidine ribonucleotides. Subsequently, the increase in
the level of dGTP stimulates the reduction of ATP to dATP. This pattern of regulation supplies
the appropriate balance of the four deoxyribonucleotides needed for the synthesis of DNA.
5.1.2 Commitment Step:

De novo synthesis of purine nucleotide occurs actively in the cytosol of the liver where all of the
necessary enzymes are present as a macro-molecular aggregate. The first step involves the
replacement of the pyrophosphate of PRPP by the amide group of glutamine. The product of this
reaction is 5-Phosphoribosylamine. The amine group which has been placed on carbon 1 of the
sugar becomes nitrogen 9 of the ultimate purine ring. This is the commitment and rate-limiting
step of the pathway.
The enzyme is under tight allosteric control by feedback inhibition. Either AMP, GMP, or IMP
alone will inhibit the amidotransferase while AMP + GMP or AMP + IMP together act
synergistically. This is a good control and probably the major factor in minute by minute
regulation of the enzyme. The nucleotides inhibit the enzyme by causing the small active
molecules to aggregate to larger inactive molecules.

[PRPP] also plays a role in regulating the rate. Normal intracellular concentrations of PRPP
(which can and do fluctuate) are below the KM of the enzyme for PRPP so there is great
potential for increasing the rate of the reaction by elevating the substrate concentration. The
kinetics are sigmoidal. The enzyme is not particularly responsive to changes in [Gln] (Kinetics
are hyperbolic and [gln] approximates KM). Very high PRPP also overcomes the normal
nucleotide feedback inhibition by causing the huge, inactive aggregates to separate back to the
small active molecules.
5.2 Purine Catabolism

Uric acid is the end product of purine catabolism in man. Other mammals such as cows, have
the enzyme urate oxidase and excrete the more soluble allantoin as the end product. Man does
not have this enzyme therefore, urate is the end product for us. Uric acid is formed mainly in the
liver and excreted by the kidney into the urine.

Nucleotides to Bases

Guanine nucleotides are hydrolyzed to the nucleoside guanosine which go through

phosphorolysis to guanine and ribose 1-P. AMP is deaminated to IMP by the enzyme
adenylate (AMP) deaminase. In the catobilsm of purine nucleotides, IMP is further hydrolyzed
by nucleotidase to inosine and then phosphorolysis to hypoxanthine.

Reactions of Nucleosides to bases

Adenosine does occur but usually arises from S-Adenosylmethionine during the course of
transmethylation reactions. Adenosine is deaminated to inosine by an enzyme adenosine
deaminase. Deficiencies in either adenosine deaminase or purine nucleoside phosphorylase
lead to two different immunodeficiency diseases by mechanisms that are not clearly understood.
With adenosine deaminase deficiency, both T and B-cell immunity is affected. The
phosphorylase enzyme deficiency affects the T cells but B cells are normal. A 4 year old girl
was treated for adenosine deaminase deficiency by genetically engineering her cells to
incorporate the gene in September, 1990. The treatment, so far, seems to be successful.

Whether or not methylated purines are catabolized depends on the location of the methyl group.
If the methyl (-CH3) is on an -NH2, it is removed along with the -NH2 and the core is
metabolized in the usual way. If the methyl is on a ring nitrogen, the compound is excreted
unchanged in the urine.

Bases to Uric Acid:

Both adenine and guanine nucleotides connect at the common intermediate xanthine.
Hypoxanthine, representing the original adenine, is oxidized to xanthine by the enzyme xanthine
oxidase. Guanine is deaminated, with the amino group released as ammonia, to xanthine. If this
process is occurring in tissues rather than the liver, most of the ammonia will be transported to
the liver as glutamine for excretion as urea.

Xanthine, like hypoxanthine, is oxidized by oxygen and xanthine oxidase with the production of
hydrogen peroxide. The urate is excreted and the hydrogen peroxide is degraded by catalase in
man. Xanthine oxidase is found in significant concentration only in liver and intestine. The
pathway to the nucleosides, possibly to the free bases, is present in many tissues.

Purine bases which are not broken down are recycled - i.e. reincorporated into nucleotides.
However, This recycling, is not sufficient to meet total body requirements and so some de novo
synthesis is essential. There are tissue differences in the ability to carry out de novo synthesis.
De novo synthesis of purines is mostly active in liver. Non-hepatic tissues generally have limited
or even no de novo synthesis. For purines, especially in the non-hepatic tissues, rely heavily on
preformed bases - those salvaged from their own intracellular turnover supplemented by bases
synthesized in the liver and delivered to tissues through the blood.

Salvaging Purines

The more important of the pathways for salvaging purines uses enzymes called
phosphoribosyltransferases (PRT): PRTs catalyze the addition of ribose 5-phosphate to the base
from PRPP to yield a nucleotide.:

Base + PRPP = Base-ribose-phosphate (BMP) + PPi

We gave already seen one example of this type of enzyme as a normal part of de novo synthesis
of the pyrimidine nucleotides, - O-PRT.

As a salvage process though, we are dealing with purines. There are two enzymes, A-PRT and
HG-PRT. A-PRT is not very necessary because we generate very little adenine. (Remember that
the catabolism of adenine nucleotides and nucleosides is through inosine). HG-PRT, though, is
important and can be inhibited by both IMP and GMP. This enzyme salvages guanine directly
and adenine indirectly. Remember that AMP is generated mainly from IMP, not from free
adenine.

"Salvage" of purines is decent in most cells because xanthine oxidase, the main enzyme in taking
the purines all of the way to uric acid, is significantly active only in liver and intestine. The bases
generated by turnover in non-hepatic tissues are not readily degraded to uric acid in those tissues
and, therefore, are available for salvage. The liver does less salvage but is very active in de novo
synthesis. Though, not so much for itself but to help supply the peripheral tissues.

Inborn errors of purine metabolism

There are different inborn errors of purine metabolism such as Adenylosuccinate lyase
deficiency, Adenosine Monophosphate Deaminase Deficiency type 1, Lesch Nyhan syndrome,
Hyperuricemia, Adenine phosphoribosyltransferase deficiency, Adenosine deaminase deficiency,
Purine nucleoside phosphorylase deficiency, Xanthinuria, Gout and Mitochondrial
neurogastrointestinal encephalopathy syndrome.
• Hyperuricemia: is an abnormally high level of uric acid in the blood, Uric acid exists
largely as urate (ion form), In the pH conditions of body fluid. It can also be defined as a
condition where serum uric acid concentrations is greater than 6 mg/dL for females,
7 mg/dL for men, and 5.5 mg/dL for youth (under 18 years old).It may not be associated
with Uricosuria (increased excretion of uric acid in urine). The amount of urate in the
body is dependant on the balance between the amount of purines ingested in food, the
amount of urate synthesised within the body and the amount of urate that is excreted in
urine or through the gastrointestinal tract.
Signs and symptoms of Hyperuricemia
• High blood levels of uric acid
• Development of gout by some people
Causes of Hyperuricemia
It can be classified into three functional types such as:
 Increased production of uric acid (high levels of purine in the diet and increased purine
metabolism). A diet rich in purine is a common but minor cause of hyperuricemia. Diet
alone generally is not enough to cause hyperuricemia (see Gout). Foods rich in
purines adenine and hypoxanthine may provoke symptoms of hyperuricemia
 Decreased excretion of uric acid (kidney disease, certain drugs, and competition for
excretion between uric acid and other molecules). The main drugs that contribute to
hyperuricemia by reduced excretion are the primary antiuricosurics. Others are
diuretics, salicylates, pyrazinamide, ethambutol, nicotinic acid, ciclosporin, 2-
ethylamino-1,3,4-thiadiazole, and cytotoxic agents.
  Both increased production and reduced excretion (high levels of alcohol
and/or fructose in the diet, and starvation). Ethanol promotes production of uric acid by
increasing production of lactic acid, hence lactic acidosis. It also increases the plasma
concentrations of hypoxanthine and xanthine through the acceleration of adenine
nucleotide breakdown, and is a possible weak inhibitor of xanthine dehydrogenase. As a
byproduct of its fermentation process, beer contributes purines. Ethanol reduces removal
of uric acid by promoting dehydration and (rarely) clinical ketoacidosis
Diagnosis of Hyperuricemia
Using blood and urine tests hyperuricemia can be detected
Treatment of Hyperuricemia
• Xanthine oxidase inhibitors: Including allopurinol, febuxostat and topiroxostat,
decrease the production of uric acid, by interfering with xanthine oxidase
• Uricosuric agents (benzbromarone, benziodarone, probenecid, lesinurad, sulfinpyrazone,
ethebencid, zoxazolamine, and ticrynafen) increase the excretion of uric acid, by reducing
the reabsorption of uric acid once it has been filtered out of the blood by the kidneys.
• Adenylosuccinate lyase deficiency is a rare autosomal recessive metabolic
disorder characterized by the appearance of
succinylaminoimidazolecarboxamide riboside (SAICA riboside) and succinyladenosine
(S-Ado) in cerebrospinal fluid, urine.
Signs and symptoms of Adenylosuccinate lyase deficiency
• Aggressive behavior
• Microcephaly
• Autism
• Brachycephaly
• Mild Cerebellar hypoplasia
• Seizures
Treatment of Adenylosuccinate lyase deficiency
• Epilepsy management with anticonvulsive drugs.
• D-ribose and uridine administration
• Ketogenic diet
• S-adenosyl-1-methionine
Adenosine monophosphate deaminase deficiency type 1 or AMPD1
This is a human metabolic disorder in which the body lacks the enzyme AMP
deaminase, in sufficient amount. The disorder was formerly known as myoadenylate
deaminase deficiency. In virtually all cases, the deficiency has been caused by single-
nucleotide polymorphism (SNP) mutation, known as rs17602729 or C34T. While it was
initially regarded as a recessive (or purely homozygous) disorder, some researchers have
reported the presence of similarly detrimental effects from the heterozygous form of the
SNP. A single-nucleotide polymorphism is a germline substitution of a
single nucleotide at a specific position in the genome and is present in a sufficiently large
fraction of the population (1% or more).
Signs and symptoms of Adenosine monophosphate deaminase deficiency type 1
• Exercise intolerance,
• Muscle pain
• Muscle cramping
Treatment of Adenosine monophosphate deaminase deficiency type 1
• Maintain strength and fitness without exercising or working to exhaustion.
• Administer ribose orally at a dose of approximately 10 grams per 100 pounds (0.2
g/kg) of body weight per day, and exercise modulation as appropriate.
• Use Creatine monohydrate
Adenine phosphoribosyltransferase deficiency
Adenine phosphoribosyltransferase deficiency is an autosomal recessive metabolic
disorder related with a alteration in the enzyme adenine phosphoribosyltransferase. The disorder
results in accumulation of the insoluble purine 2,8-dihydroxyadenine. It can result
in nephrolithiasis (kidney stones), acute renal failure and permanent kidney damage. Patients
with the disease disorder lack the enzyme adenine phosphoribosyltransferase and therefore have
difficulties degrading dietary substances called purines, resulting in accumulation of a compound
called 2,8-dihydroxyadenine (2,8-DHA) that is excreted by the kidneys. Up to 70% of affected
patients, have red hair or relatives with this hair colour.
Signs and symptoms of Adenine phosphoribosyltransferase deficiency
• Development of kidney stones
• Fever
 • Urinary tract infection
• Blood in the urine (hematuria)
• Abdominal cramps
• Nausea
• Vomiting

• Adenosine deaminase deficiency (ADA deficiency)

Adenosine deaminase deficiency is a metabolic disorder that causes immunodeficiency.

It is caused by mutations in the ADA gene. It accounts for about 10–15% of many cases
of autosomal recessive forms of severe combined immunodeficiency (SCID) among non-
inbred populations. On chromosome 20, the enzyme adenosine deaminase is encoded by
the ADA gene on chromosome 20. ADA deficiency is inherited in an autosomal
recessive manner. This means that the faulty gene responsible for the disorder is located
on an autosome (chromosome 20 is an autosome), and two copies of the faulty gene (one
inherited from each parent) are required in order to be born with the disorder. The parents
of an individual with an autosomal recessive disorder carries both one copy of the faulty
gene, but usually do not experience any signs or symptoms of the disorder

Signs and symptoms of Adenosine deaminase deficiency

• Pneumonia

• Chronic diarrhea

• Widespread skin rashes

Treatment of Adenosine deaminase deficiency

• Bone marrow transplant
• ADA enzyme in PEG vehicle
• Gout

Gout is a form of inflammatory arthritis distinguished by recurrent attacks of a red, tender, hot
and swollen joint, caused by the accumulation of needle-like crystals of uric acid known
as monosodium urate crystals. Pain usually comes on quickly, reaching maximal intensity in less
than 12 hours. The joint at the base of the big toe is affected (Podagra) in about half of cases. It
could also result in tophi, kidney stones, or kidney damage.

Gout is as a result of the consistent elevated levels of uric acid (urate) in the blood
(hyperuricemia). This happen from a combination of diet, other health problems, and genetic
factors. At high levels, uric acid crystallizes and the crystals deposit in joints, tendons, and
surrounding tissues, resulting in an attack of gout. Gout occurs commonly in those who drink
beer or sugar-sweetened beverages regularly; eat foods that are rich in purines such as liver,
shellfish, or anchovies; or are overweight. Diagnosis of gout may be confirmed by the existence
of crystals in the joint fluid or accumulate outside the joint. Blood uric acid levels may be normal
during an attack.

Treatment with nonsteroidal anti-inflammatory drugs (NSAIDs), glucocorticoids,

or colchicine improves symptoms. Once the severe attack subsides, levels of uric acid can be
reduced through lifestyle changes and in those with regular
attacks, allopurinol or probenecid provides long-term prevention. Taking vitamin C and eating a
diet high in low-fat dairy products may be preventive.

Gout affects about 1 to 2% of adults in the developed world at some point in their lives. It has
become more common in recent [Link] is believed to be due to increasing risk factors in
the population, such as metabolic syndrome, longer life expectancy, and changes in diet. Older
males are most commonly affected . Gout was historically known as "the disease of kings" or
"rich man's disease".It has been recognized at least since the time of the ancient Egyptians.

Signs and symptoms of Gout

• Recurrent attack of acute inflammatory arthritis (a red, tender, hot, swollen joint).

• The metatarsophalangeal joint at the base of the big toe is affected most often,
accounting for half of cases.

• Other joints, such as the heels, knees, wrists, and fingers, may also be affected.

• Joint pain usually begins during the night and peaks within 24 hours of onset. This is
mainly due to lower body temperature.

• Fatigue
 • High fever.

• Chronic arthritis due to bone erosion.

• Formation of kidney stomes

Causes of Gout

The crystallization of uric acid, often associated to relatively high levels in the blood, is the main
cause of gout. This might occur because of diet, genetic predisposition, or underexcretion
of urate, the salts of uric acid. Underexcretion of uric acid by the kidney is the primary cause of
hyperuricemia in about 90% of cases, while overproduction is the cause in less than 10%. About
10% of people with hyperuricemia develop gout at some point in their lifetimes. The risk can
vary depending on the degree of hyperuricemia. When levels are between 415 and 530 μmol/L (7
and 8.9 mg/dl), the risk is 0.5% per year, while in those with a level greater than 535 μmol/L
(9 mg/dL), the risk is 4.5% per year

Prevention of Gout

• Complete abstinence from drinking alcoholic beverages.

• Reducing the intake of fructose (e.g. high fructose corn syrup)

• Reduce purine-rich foods of animal origin, such as organ meats and seafood.

• Eating dairy products, vitamin C-rich foods, coffee, and cherries may help prevent gout
attacks, as does losing weight.

• Apply ice for 20 to 30 minutes several times a day to decrease pain

• The following drugs such as allopurinol, febuxostat, and probenecid can also be used.

7. Lesch–Nyhan syndrome (LNS)

Lesch–Nyhan syndrome (LNS) is a uncommon inherited disorder caused by a deficiency of

the hypoxanthine-guanine phosphoribosyltransferase (HGPRT). This deficiency occurs due
to mutations in the HPRT1 gene which is found on the X chromosome. LNS affects about 1 in
380,000 births. Lesch–Nyhan syndrome was first recognized and clinically characterized by
American medical student Michael Lesch and his mentor, pediatrician William Nyhan, at Johns
Hopkins.
The HGPRT deficiency causes a build-up of uric acid in all body fluids. The combination of
elevated synthesis and reduced utilization of purines leads to high levels of uric acid production.
This results in both high levels of uric acid in the blood and urine, interrelated with
severe gout and kidney problems. Neurological signs include poor muscle control and
moderate intellectual disability. These complications normally appear in the first year of life.
Beginning in the second year of life, a particularly striking feature of LNS is self-
mutilating behaviors, characterized by lip and finger biting. Neurological symptoms may include
facial grimacing, involuntary writhing, and repetitive movements of the limbs similar to those
seen in Huntington's disease. The cause of the neurological abnormalities remains unknown. A
lack of HGPRT causes the body to poorly utilize vitamin B, it could lead to megaloblastic
anemia in some males

LNS is inherited in an X-linked recessive manner; the gene mutation is normally carried by the
mother and passed on to her son, although one-third of all cases arise de novo (from new
mutations) and do not have a family history. LNS is usually present at birth in baby boys. Most
persons with this deficiency have severe mental and physical problems throughout life. Cases in
females are very rare.

Signs and symptoms of Lesch–Nyhan syndrome

• Overproduction of uric acid

• Impairment of Nervous System

• Self-injury behavior (self-mutilation)

• Increase uric acid excretion in females

• Formation of Gout and kidney stones.

Inborn errors of pyrimidine metabolism

• Orotic aciduria

Orotic aciduria is a disease caused by an enzyme deficiency resulting in a reduced ability to

synthesize pyrimidines. It was the first described enzyme deficiency of the de novo pyrimidine
synthesis pathway.
Orotic aciduria is indicated by excessive excretion of orotic acid in urine because of the inability
to convert orotic acid to UMP. It causes megaloblastic anemia and may be linked with mental
and physical developmental delays. This autosomal recessive disorder is caused by a deficiency
in the enzyme UMPS, a bifunctional protein that includes the enzyme activities
of OPRT and ODC. In a study of three patients, UMPS activity ranged from 2-7% of normal
levels. Two types of orotic aciduria have been reported. Type I has a severe deficiency of both
activities of UMP synthase. In Type II orotic aciduria, the ODC activity is deficient while OPRT
activity is increased. Since 1988, only one case of type II orotic aciduria had ever been reported.
Orotic aciduria is related with megaloblastic anemia due to reduced pyrimidine synthesis, which
leads to decreased nucleotide-lipid cofactors needed for erythrocyte membrane synthesis in the
bone marrow

Signs and symptoms of Orotic aciduria

• Orotic acid in the urine

• Failure to thrive

• Developmental delay

• Megaloblastic anemia

Treatment of Orotic aciduria

Administration of uridine monophosphate (UMP) or uridine triacetate which is then converted to

UMP. These medications will bypass the missing enzyme and provide the body with a source of
pyrimidines.

• Dihydropyrimidine dehydrogenase deficiency

Dihydropyrimidine dehydrogenase deficiency is an autosomal recessive metabolic disorder in

which there is absent or decreased activity of dihydropyrimidine dehydrogenase which is an
enzyme involved in the metabolism of uracil and thymine. Individuals with this condition might
develop life-threatening toxicity as a result of exposure to 5-fluorouracil (5-FU),
a chemotherapy drug which is used in the treatment of cancer. Beside 5-FU, widely prescribed
oral fluoropyrimidine capecitabine (Xeloda) could put DPD-deficient patients at risk of
experiencing very severe or lethal toxicities as well.
Pyrimidine Synthesis:

Pyrimidine synthesis occurs in a variety of tissues. Since pyrimidine molecules are simpler than
purines, so is their synthesis simpler but is still from readily available components. The amide
nitrogen in glutamine and carbon dioxide provide atoms 2 and 3 or the pyrimidine ring. They do
so, however, after they have been converted to carbamoyl phosphate. The other four atoms of the
ring are supplied by aspartate. As is true with purine nucleotides, the sugar phosphate part of the
molecule is supplied by PRPP.

6.1 Carbamoyl Phosphate

Pyrimidine synthesis starts with carbamoyl phosphate synthesized in the cytosol of those tissues
capable of making pyrimidines which are highest in spleen, thymus, GItract and testes. This uses
a different enzyme than the one involved in urea synthesis. Carbamoyl phosphate synthetase II
(CPS II) prefers glutamine to free ammonia and has no need for N-Acetylglutamate.
6.2 Formation of Orotic Acid

Carbamoyl phosphate condenses with aspartate in the presence of aspartate transcarbamylase to

give rise to N-carbamylaspartate which is then converted to dihydroorotate.

CPSII, asp-transcarbamylase, and dihydroorotase activities are part of a multifunctional protein

in man.

Oxidation of the ring by a complex, poorly understood enzyme produces the free pyrimidine,
orotic acid. This enzyme is found on the outer face of the inner mitochondrial membrane, in
contrast to the other enzymes which are cytosolic. Note the difference with purine synthesis in
which a nucleotide is formed first while pyrimidines are first synthesized as the free base.

6.3 Regulation of Pyrimidine Synthesis:

In man, the control of pyrimidine nucleotide synthesis is exerted primarily at the level of
cytoplasmic CPS II. UTP inhibits the enzyme, competitively with ATP. PRPP activates it. Other
secondary sites of control also exist (e.g. OMP decarboxylase is inhibited by UMP and CMP).
These are probably not important under normal circumstances.

In bacteria, aspartate transcarbamylase is the control enzyme. There is only one carbamoyl
phosphate synthetase enzyme in bacteria since they do not have mitochondria. Carbamoyl
phosphate rather participates in a branched pathway in these organisms that leads to either
pyrimidine nucleotides or arginine.

Pyrimidine Catabolism

Unlike purines, pyrimidines undergo ring cleavage and the usual end products of catabolism are
beta-amino acids plus ammonia and carbon dioxide. Pyrimidines from nucleic acids or the
energy pool are acted upon by nucleotidases and pyrimidine nucleoside phosphorylase to give
rise to free bases. The 4-amino group of both cytosine and 5-methyl cytosine is released as
ammonia.

Ring Cleavage

In order for the rings to be split, they must first be reduced by NADPH. Atoms 2 and 3 of both
rings are released as ammonia and carbon dioxide. The rest of the ring is left as a beta-amino
acid. Beta-amino isobutyrate from thymine or 5-methyl cytosine is largely removed from the
system. Beta-alanine from cytosine or uracil may either be excreted or assimilated into the brain
and muscle dipeptides, carnosine (his-beta-ala) or anserine (methyl his-beta-ala).
Salvaging Pyrimidines

The other type of salvage pathway involves two steps and is the major pathway for the
pyrimidines, uracil and thymine.

Base + Ribose 1-phosphate = Nucleoside + Pi (nucleoside phosphorylase)

Nucleoside + ATP - Nucleotide + ADP (nucleoside kinase - irreversible)

There is a uridine phosphorylase and kinase and a deoxythymidine phosphorylase and a

thymidine kinase that can salvage some thymine in the presence of dR 1-P.

Formation of Deoxyribonucleotides

De novo synthesis and most salvage pathways involves the ribonucleotides. An exception is the
small amount of salvage of thymine indicated above. Deoxyribonucleotides which are for DNA
synthesis are formed from the ribonucleotide diphosphates (in mammals and E. coli).

A base diphosphate (BDP) is reduced at the 2' position of the ribose portion using a protein,
thioredoxin and an enzyme nucleoside diphosphate reductase. Thioredoxin has two sulfhydryl
groups which are oxidized to a disulfide bond during this process. In order to restore the
thioredoxin to its reduced for so that it can be recycled, thioredoxin reductase and NADPH are
required.

This system is tightly controlled by a variety of allosteric effectors. dATP is a general inhibitor
for all substrates and ATP an activator. Each substrate then has a particular positive effector (a
BTP or dBTP). Which results in the maintenance of an appropriate balance of the
deoxynucleotides for DNA synthesis.

Synthesis of dTMP

DNA synthesis also requires dTMP (dTTP). Which is not synthesized in the de novo pathway
and salvage is not adequate to maintain the necessary amount. dTMP is gotten from dUMP using
the folate-dependent one-carbon pool.

Since the enyme nucleoside diphosphate reductase is not very active toward UDP, CDP is
reduced to dCDP and then converted to dCMP. This is then deaminated to form dUMP. In the
presence of 5,10-Methylene tetrahydrofolate and the enzyme thymidylate synthetase, the
carbon group is both passed on to the pyrimidine ring and further reduced to a methyl group. The
other product is dihydrofolate which is eventually reduced to the tetrahydrofolate by
dihydrofolate reductase.
Chemotherapeutic Agents

Thymidylate synthetase is specifically sensitive to availability of the folate one-carbon pool.

Some of the cancer chemotherapeutic agents interfere with this process as well as with the steps
in purine nucleotide synthesis which involves the pool.

Cancer chemotherapeutic agents like methotrexate (4-amino, 10-methyl folic acid) and
aminopterin (4-amino, folic acid) are structural analogs of folic acid and inhibit the enzyme
dihydrofolate reductase. This obstruct the maintenance of the folate pool and thus of de novo
synthesis of purine nucleotides and of dTMP synthesis. Such agents are very toxic and
administered under careful control.
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