Central Dogma of Biology

Nucleic Acids Are Essential For Information Transfer in Cells

Information encoded in a DNA molecule is transcribed via synthesis of an RNA molecule

The sequence of the RNA molecule is "read" and is translated into the sequence of amino acids in a protein.

Compound contained C, N, O, and high amount of P.

Was an acid compound found in nuclei therefore named nucleic acid

1944 Oswald, Avery, MacLeod and McCarty demonstrated that DNA is the molecule that carrier genetic information.

1953 Watson and Crick proposed the double helix model for the structure of DNA Nucleic acids are long polymers of nucleotides.

Nucleic Acids

Nucleotides and Nucleic AcidsThe amino acids sequence and nucleotide sequence in RNA is

specified by a nucleotide sequence in the cell’s DNA

Gene: segment of a DNA molecule that contains the information

required for the synthesis of a functional biological product whether

a protein or RNA

The cell contains thousands of genes and DNA molecules

Nucleic Acids are polymers of

nucleotides.

Deoxyribonucleic acid - DNA - Storage

of genetic information.

Ribonucleic acid - RNA - carriers of

genetic information and catalysis.

Nucleotide Structure: Nitrogenous

base + ribose phosphate:

Nucleotides structureThe nucleotide has three characteristic components Nitrogenous basePentose sugarPhosphate

Nitrogenous Bases

Nitrogenous base: derivatives of Purines and pyrimidines

DNA and RNA contain the same purine bases and the pyrimidine base

Cytosine But Thymine found only in DNA and Uracil found only in

RNA

(A) (G)

(C) (T)(U)

Pentoses of Nucleotides

• D-ribose (in RNA) • 2-deoxy-D-ribose (in

DNA) • The difference - 2'-

OH vs 2‘-H • This difference

affects secondary structure and stability

Bases are attached by -N-glycosidic linkages to 1 carbon of pentose sugar – (Nucleoside)

• Base is linked via a -N-

glycosidic bond

• The carbon of the

glycosidic bond is

anomeric

• Named by adding -idine

to the root name of a

pyrimidine or -osine to

the root name of a

purine

• Sugars make

nucleosides more water-

soluble than free bases

Nucleosides

(9)

(1)

Nucleotides• Phosphate ester of nucleosides

The plane of the base is oriented perpendicular to the plane of the pentose group

RNA contains Ribose while DNA contains 2'deoxy-D-Ribose

Nucleoside: Nitrogenous base + ribose:

Ribonucleotides

Adenosine 5'-monophosphate, Adenylate, AMP

Guanosine 5'-monophosphate, Guanylate, GMP

Cytidine 5'-monophosphate, Cytidylate, CMP

Uridine 5'-monophosphate, Uridylate, UMP

Deoxyribonucleotides

Deoxythymidine 5' monophosphate,

Deoxythymidine, dTMP ……..

NMP=== Nucleoside mono phosphate.

Numbering of Ribose sugar is given 1’, 2’, …, 5’

Unusual nucleotides Modified nucleotides found in some viral DNA and in Transfer RNA. These modifications include methylation, hydroxymethylation, glycosylation, acetylation ..

Other Functions of Nucleotides

• Nucleoside 5'-triphosphates are carriers of energy

• Bases serve as recognition units • Cyclic nucleotides are signal molecules and

regulators of cellular metabolism and reproduction

• Structural component of some coenzymes, e.g CoA, FAD, NADH, NADPH

• ATP is central to energy metabolism • GTP drives protein synthesis • CTP drives lipid synthesis • UTP drives carbohydrate metabolism

N10Formyl tetrahydrofolate

De novo synthesis of purine nucleotides

The atoms of purine ring are contributed by a number of compounds

including amino acids (aspartic acid, glycine and glutamine) CO2,

and tetrahydrofolate. These compounds donates N and C to

constructed Ribose 5-phosphate.

93

2

1

65

4

7

8

NN1

2N

3

6

4

5 7

8N

9

Ribose-P

The order in which ring atoms are added is:

9 4 5 7 8 3 6 1 2

Glut Glycine For Glut CO2 Asp For

De novo synthesis of purine nucleotides * Synthesis of 5-phosphoribosyl-1-pyrophosphate (PRPP)

-Ribose 5-phosphate is synthesized from HMP (Hexose

monophosphate pathway)

- Ribonucleotides are first synthesized then may reduced to

deoxyribonucleotides

Ribose5-

phosphate

Ribose phosphate pyrophosphokinase

ATP AMP

Activator Pi

InhibitorsPurines,

nucleosides

* Synthesis of 5-phosphoribosyl-1-pyrophosphate

(PRPP)•The amide group of the glutamine replaces pyrophosphate group

attached to PRPP, this reaction is mediated by

Glutamine:phosphoribosyl pyrophosphate amidotransferase.

•This enzyme is inhibited

by end product of this

pathway purine 5’-

nucleotides AMP, GMP

and IMP.

• This reaction is the

committed step in purine

nucleotide synthesis

De novo synthesis of purine nucleotides

* Synthesis Inosine

monophosphate (IMP)• IMP is the parent purine nucleotide

•the synthesis of IMP requires 4 ATP

molecules

Inhibitors of Purine synthesis

•Specific inhibitors that inhibits the

growth of rapidly growing

microorganisms e.g Sulfonamides

•Structural analogues for folic acid

(methotroxate)

* Conversion of IMP into AMP and GMP-this reaction is energy-requiring pathway

Adenylosuccinate synthetase

IMP dehydrogenase

Feed back inhibition

Feed back inhibition

Conversion of IMP into AMP and GMP

* Conversion Nucleoside momophosphate (NMP) to

nucleoside diphosphate (NDP) and triphosphate

(NTP)

•NDP and NTP are synthesized from the corresponding NMP

by Nucleoside monophosphate kinases

•These kinases don't discriminate between ribose or

deoxyribose in the substrate.

•ATP is the source of the transferred phosphate

examples

AMP + ATP 2 ADP adenylate kinase (highly active in

the liver)

GMP + ATP GDP + ADP Guanylate kinase

Nucleoside diphosphates and triphosphates are

interconverted by nucleoside diphosphate kinase

GDP + ATP GTP + ADP

CDP + ATP CTP + ADP

De novo synthesis of purine

nucleotides

Two enzymes are involved Adenine phosphoribosyl

transferase (APRT)Hypoxanthine-guanine

phosphoribosyl transferase

(HGPRT)

Both enzymes utilize PRPP as the

source of ribose5-phosphate

group

Salvage Pathway for Purines

Salvage Pathway: Purines that results from the normal turnover of cellular

nucleic acids or that obtained from the diet and not degraded can be

reconverted into nucleoside triphosphates and used by the body.

Degradation of Purine nucleotides

Degradation of Purine nucleotides Purines are sequentially degraded into uric acids (in

humans) Several steps will be involved in this catabolic pathway

Degradation of Dietary nucleic acids in the small

intestine

• Ribonucleases and deoxyriboncleases secreted in the

pancreatic juice can hydrolyze RNA and DNA into

oligonucleotides.

• Oligonucleotides are further hydrolyzed by pancreatic

phophodiesterases producing a mixture of 3’-and 5’

mononucleotides

• A family of nucleotidases remove the phosphate group

releasing nucleosides that may absorbed from GIT

• Dietary nucleotides are not used to large extent in cells

because they are converted into uric acid in the small

intestine and also used by the normal flora

Degradation of Purine nucleotides

Pyrimidine nucleotides synthesisSources of carbon atoms in pyrimidine ringsPurine ring is synthesized on an existing ribose 5-phosphate

Pyrimidine ring is synthesized then attached to ribose 5-phosphate

donated by PRPP

the sources of carbon atoms in pyrimidine rings are Glutamine, CO2,

and aspartic acid

Aspartic Acid

Amide

Nitrogen of

Glutamine

CO2

De Novo Pyrimidine Synthesis

Pyrimidine nucleotides synthesis- *Synthesis of carbamoyl phosphate

-The committed step of this pathway in mammalian cell is the

synthesis of carbamoyl phosphate from Glutamine and CO2

2 ATP + CO2 + Glutamine Carbamoyl phosphate + 2ADP +

Glutamate

- This reaction is mediated by Carbamoyl Phosphate Synthetase II

(CPS II)

- CPS II is inhibited by UTP and activated by ATP and PRPP

- Carbamoyl phosphate is the precursor of Urea; the pyrimidine

synthesis occurs in the cytosol while the urea production occurs in

the mitochondria by Carbamoyl Phosphate Synthetase I (CPS I)

- CPS I uses ammonia as source of nitrogen

- CPS II uses the amide group of glutamine

- Glutamine is required in the synthesis

of both Purines and Pyrimidine

Synthesis of carbamoyl phosphate

De Novo Pyrimidine Synthesis

Degradation of pyrimidines- Purines are not cleaved in human cell

- pyrimidines rings can be opened and degraded to

highly soluble structure, such as -alanine and -

aminoisobutyrate that can serve as precursors of acetyl

CoA and succinyl CoA

- Pyrimidine can be salvaged and converted into

nucleotides by the enzyme Pyrimidine

phosphoribosyltransferase and it utilizes the PRPP

Conversion of Ribonucleotides to

Deoxyribonucleotides 2’-deoxyribonucleotides are synthesized from ribonucleoside

diphosphatase Ribonucleotide reductase is multi subunit enzyme (2B1 and

2B2 subunits) catalyzes the reduction of NDP (ADP, GDP, CDP,

UDP) into dNDP (dADP, dGDP, dCDP, dUDP) The immediate donors of hydrogen atoms needed for the

reduction are two–SH groups of the enzyme itself The reduced form of the enzyme should be regenerated The

reducing agent is a peptide coenzyme of ribonucleotide reductase

called Thioredoxin The thioredoxin contain two cysteine residues that can be

oxidized to reduce the ribonucleotide reductase enzyme. The oxidized thioredoxin is reduced back by NADPH, this reaction

is mediated by Thioredoxine reductase

Synthesis of Thymidine

monophosphate from dUMP-dUMP is converted into dTMP by

thymidylate synthetase which

utilizes N5 N10 –methylene

tetrahydrofolate as the source of

methyl group and 2 hydrogen

oxidation into dihydrofolate.

- inhibitors of thymidylate

synthetase (5-flouro uracil) act as

anti-tumor

- DHF can be reduced into THF by

DHF reductase, which can be

inhibited by Methotrexate

inhibits purine synthesis and

decrease the supply of THF so

prevents methylation of dUMP to

dTMP

The End

Regulation of Deoxyribonucleotides synthesis The regulation of this enzyme is complexNot only the activity is regulated but also substrate specificityThe binding of dATP to an allosteric site called activity site inhibits the enzyme while the binding of ATP to this site activate the enzyme.The binding of NTP to an allosteric site called substrate specificity will increase the conversion of different NTP to their corresponding dNTP according to the need of the cell

When ATP or dATP are bound to this site reduction of UDP, and CDP is favored When dTTP,or dGTP is bound the reduction of GDP, ADP is stimulated

Anti- conformation predominates in nucleic acid polymers

•Conformation can be syn or anti

Nitrogenous base: derivatives of Purines and pyrimidines

DNA and RNA contain the same purine bases and the

pyrimidine base Cytosine But Thymine found only in DNA and

Uracil found only in RNA

(A) (G)

(C)(T) (U)