NUCLEOTIDE METABOLISM

NUCLEOTIDES

Nucleotides are essential for all cells They are main building blocks of DNA and RNA and without them proteins cannot be synthesized or cells cannot proliferate Nucleotides serve as carriers of activated intermediates in the synthesis of some macromolecules They are structural components of essential co-enzymes such as coenzyme A, FAD, NAD, and NADP Nucleotides play an important role as energy currency in the cell

Types Of Bases:
1. Purine Bases 2. Pyrimidine bases 3. Unusual bases

NUCLEOSIDES:
Ribose Sugar (Pentose) + Nitrogenous Base

NUCLEOTIDES:
Ribose Sugar + Nitrogenous Base + Phosphoryl Group

NUCLEIC ACIDS:
polymer of nucleotides storage & expression of genetic information

TYPES OF NUCLEOSIDES

Ribonucleosides:

Contains Ribose Sugar

Deoxyribonucleosides:

Contains Deoxyribose sugar

TYPES OF NUCLEOTIDES

Ribonucleotides:

Contains Ribose Sugar

Deoxyribonucleotides:

Contains Deoxyribose sugar

TYPES OF NUCLEIC ACIDS

RNA (Ribonucleic acid) :

Polymer of Ribonucleotides

DNA (Deoxyribonucleic acid):

Polymer of Deoxyribonucleotides

PURINE BASES
1. 2.

ADENINE ( A ) GUANINE ( G ) Present In Both DNA & RNA Larger Heterocyclic Bases Contain 9 Atoms 4N+5C of Counterclockwise numbering atoms in ring

STRUCTURE OF PURINE
H C 6 N7 C5 CH 8 C2 C4 N3

N1

N H9

Sum Up Structure As
1 2 3 N C N 4 5 6 C C C 7 8 N C 9 N

PURINE
ADENINE (A) NH2
6

GUANINE (G) O
6

HN
2

N H

NH2

N H

6 - Aminopurine

2 Amino -6 - oxypurine

2.PYRIMIDINE BASES
1. 2. 3.

THYMINE (T) CYTOSINE (C) URACIL (U)

RNA = Cytosine & Uracil DNA = Cytosine & Thymine Smaller Heterocyclic Bases Contain 6 Atoms ---- 2 N + 4 C Clockwise numbering of atoms in the ring

Structure Of Pyrimidine H C4
N
3

CH

HC 2

CH 6

N1

O
4

PYRIMIDINES
O
4

HN O
2

HN N H Uracil (U) 2,4 Dioxy pyrimidine O

2

CH3

NH2
4

N
2

N H Thymine (T) (5-methyl Uracil)

N H

Cytosine (C) (2-oxy,4-amino pyrimidine)

Linkage Between Base & Ribose Sugar

N Glycosidic Bond 1/ C linked to N-1 of Pyrimidine and N-9 of purine base

Cytidine (cytosine + ribose sugar)

NH2
3 4 5 2 6 N

N O OH
4
/

5/

1/
3/ 2/

OH

OH

Nucleosides If a sugar, either ribose or 2-deoxyribose, Nucleic to a nitrogen base, the resulting is added Acid compound is called a nucleoside. Carbon 1 of the sugar is attached to nitrogen 9 of a purine base or to nitrogen 1 of a pyrimidine base. Adenosine Guanosine Inosine - the base in inosine is hypoxanthine Uridine Thymidine Cytidine

Nucleotides Adding one or more phosphates to the sugar Nucleic Acid portion of a nucleoside results in a nucleotide. Generally, the phosphate is in ester linkage to carbon 5' of the sugar. AMP = adenosine monophosphate = adenylic acid CDP = cytidine diphosphate dGTP = deoxy guanosine triphosphate dTTP = deoxy thymidine triphosphate (TTP) cAMP = 3'-5' cyclic adenosine monophosphate

Polynucleotides

Nucleotides are joined together by 3'-5' phosphodiester bonds to form polynucleotides. Polymerization of ribonucleotides will produce an RNA while polymerization of deoxyribonucleotides leads to DNA.

Deoxyribonucleic acid

DNA is a polymer of deoxyribonucleotides It is found in chromsomes, mitochondria and chloroplasts Primary structure It is number and sequence of different deoxyribonucleotides in its strands joined by phosphodiester linkage

PURINE
ADENINE (A) NH2
6

GUANINE (G) O
6

HN
2

N H

NH2

N H

6 - Aminopurine

2 Amino -6 - oxypurine

O
4

PYRIMIDINES
O
4

HN O
2

HN N H Uracil (U) 2,4 Dioxy pyrimidine O

2

CH3

NH2
4

N
2

N H Thymine (T) (5-methyl Uracil)

N H

Cytosine (C) (2-oxy,4-amino pyrimidine)

NH2
3 4 5 2 6 N

N O OH
4
/

5/

1/
3/ 2/

OH

OH

Deoxyribonucleic acid

Secondary structure Double helix The edge of he helix that measures more than 180 from glycosidic bond to glycosidic bond is called the major groove and if it is less than 180 it is called minor groove Three types of conformation have been found

B-DNA A-DNA Z-DNA

B-DNA

Adjacent nucleotides in each chain are rotated by 34.6 relative to each other One turn approximately completes after every10.4 base pairs One turn spans the distance of 3.4 nM This is called pitch of DNA Diameter of double helix is 2.37nM

A-DNA

When B-DNA crystals are dried or when salt content of the crystals is lowered, the long thin DNA molecule becomes short, stubby molecule and is called ADNA

Z-DNA

It is longer and thinner than B-DNA It has left handed helix One complete turn has 12 base pairs Diameter is 1.84 nM The major groove is no more but a convex surface Minor groove is in form of a cleft

Ribonucleotides

m-RNA hn-RNA PRE-mRNA r-RNA t-RNA

Messenger RNA

5-10% of cellular RNA is a molecule of RNA that encodes a chemical "blueprint" for a protein product. mRNA is transcribed from a DNA template, and carries coding information to the sites of protein synthesis, the ribosomes. In the ribosomes, the mRNA is translated into a polymer of amino acids : a protein

Transfer RNA

10-15% of cellular RNA Transfers amino acids to the ribosomes for protein synthesis

Ribosomal RNA

75-80% of cellular RNA Found in ribosomes which are the sites of protein synthesis

SYNTHESIS OF PURINE NUCLEOTIDES

DE NOVO SYNTHESIS SALVAGE PATHWAY FOR PURINES

STRUCTURE OF PURINE
H C 6 N7 C5 CH 8 C2 C4 N3

N1

N H9

Sum Up Structure As
1 2 3 N C N 4 5 6 C C C 7 8 N C 9 N

SOURCE OF 4 NITROGEN ATOMS

GLUTAMINE GLYCINE ASPARTATE 2 N ( 3, 9 ) 1N(7) 1N(1)

SOURCE OF 5 CARBON ATOMS

N10 FORMYLE THF GLYCINE CO2 2 C ( 2, 8 ) 2 C ( 4, 5 ) 1C(6)

SUBSTRATE TO START:

Ribose 5 /- Phosphate (HMP-Shunt)

Sources of the individual atoms in the Pyrimidine ring

Amide nitrogen of glutamine C N C N C C

Aspartic acid

CO2

Source Of 2 Nitrogen Atoms

Glutamine Aspartic Acid 1N 1N (3) (1)

Source of 4 carbon atoms

Aspartic Acid ( 4,5,6 ) CO 3C 1C (2)

Pyrimidine Biosynthesis PRECURSORS

1). PRPP (donor of Ribose-5-PO4) 2). Glutamine 3). CO2 4). Aspartate

KEY ENZYME
Carbamoyl Phosphate Synthase II (Cytosolic )

Six membered Pyrimidine ring is synthesized and then attached to Ribose 5 phosphate, unlike purines Glutamine and aspartate are required for both purine and pyrimidine synthesis

SALVAGE PATHWAY FOR PURINES

DEFINITION Free purine bases obtained due to Breakdown of nucleic acids or from the diet and not degraded, can be reconverted into Nucleoside triphosphates (nucleotides) and used by the Body. Requires less energy

ENZYMES REQUIRED
1.

Adenine Phosphoribosyl Transferase ( APRT )

2.

Hypoxanthine Guanine Phosphoribosyl Transferase ( HGPRT )

SOURCE OF RIBOSE 5 PHOSPHATE:

Phosphoribosyl Pyrophosphate ( PRPP )

SUBSTRATES FOR SALVAGE PATHWAY

HYPOXANTHINE GUANINE

REACTIONS OF SALVAGE PATHWAY

PRPP PPi

HYPOXANTHINE LESCH NYHAN SYNDROME HGPRT

PRP P PPi

IMP

GUANIN E ADENIN E

HGPRT
PRPP PPi

GM P AMP

APRT

Salvage of Pyrimidine
Substrate Enzyme

Uridine Cytidine
Uridine Cytidine kinase

Deoxycytidine Deoxycytidine kinase Thymidine Thymidine kinase

ATP

ADP

Uridine
Uridine-Cytidine Kinase

UMP CMP

Cytidine

ATP ATP

ADP ADP

Thymidine

Thymidine Kinase ADP ATP Deoxycytidine Kinase

TMP dCMP

Deoxycytidine

Metabolic disorders of nucleotides

Leisch-Nehan Syndrome Gout Orotic aciduria Xanthineuria

Degradation of purine nucleotides

Normal plasma uric acid level: Men: 3 9 mg/dl Woman: 2.5 7.5 mg/dl

Degradation of Pyrimidines

Produces NH4+ and thus urea formation Unlike purines, its ring structure can be opened/cleaved into highly water soluble structures like - Alanine (a precursor of acetyl-CoA) -Aminoisobutyrate (a precursor of Succinyl-CoA)

CPS I
Cellular location Pathway involved Source of Nitrogen mitochondria Urea cycle Ammonia

CPS II
cytosol Pyrimidine synthesis -Amide group of glutamine

Digestion and absorption of nucleotides

Nucleotidases break down nucleotides (such as the thymidine monophosphate ) into nucleosides (such as thymidine) and phosphate. The nucleosides, in turn, are subsequently broken down in the lumen of the digestive system by nucleosidases into nitrogenous bases and ribose or deoxyribose

Chromosomes

A chromosome is an organized structure of DNA and protein found in cells. It is a single piece of coiled DNA containing many genes, regulatory elements and other nucleotide sequences. Chromosomes also contain DNA-bound proteins, which serve to package the DNA and control its functions.

Chromatin

In eukaryotes, nuclear chromosomes are packaged by proteins into a condensed structure called chromatin.

Genes

A gene is a molecular unit of heredity of a living organism. It is a name given to some stretches of DNA and RNA that code for a polypeptide or for an RNA chain that has a function in the organism. Living beings depend on genes, as they specify all proteins and functional RNA chains.

Gene expression

Gene expression is the process by which information from a gene is used in the synthesis of a functional gene product. These products are often proteins, but in non-protein coding genes such as ribosomal RNA (rRNA), transfer RNA ( tRNA) or small nuclear RNA (snRNA) genes, the product is a functional RNA.