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In-Class Powerpoints

LECTURE TOPICS: Building Blocks of Nucleic Acids

PURINE & PYRIMIDINE NUCLEOTIDES:   STRUCTURESAND NOMENCLATURE

HOW ARE NUCLEOTIDES FOR DNA AND RNA MADE?

 

RIBONUCLEOTIDES FOR RNA	DEOXYRIBONUCLEOTIDES FOR DNA
(AMP + GMP) from common source:  de novo synthesis	Ribonucleotide reductase for (A, G, C)
(UMP) first then CTP	thymidylate synthase for (T)

INTERCONVERSIONS OF NUCLEOTIDES:  Phosphate exchanges

• NUCLEOTIDE ANALOG DRUGS WHICH INHIBIT NUCLEOTIDE SYNTHESIS

                 • uses in cancer and virus chemotherapy


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Chapter25 Learning Objectives

KEY CONCEPTS:

• Know the nucleotide structures and nomenclature cold!
• Nucleotides or nucleotide derivatives play key roles in many biochemical processes.
• Purine and pyrimidine bases, 5-carbon sugars (ribose for RNA) and 2-deoxyribose (For DNA), and phosphate are the building blocks of nucleic acids.
• Phosphorylation states (one, two, or three phosphates) of nucleotides can be interconverted by enzymes which permit nucleotides to exhange phosphate groups.
• Nucleoside triphosphate forms of the four ribonucleotides(for RNA) and the four deoxyribonucleotides (for DNA) are the activated substrates required for RNA and DNA synthesis.
• Some key points about synthesis of nucleotides for RNA and DNA are:
1] UMP is made first and then CTP is made from UTP.
2]AMP and GMP are made from the common precursor IMP
3]dTMP is synthesized from dUMP.
4]Deoxyribonucleotides are synthesized from ribonucleotides by ribonucleotide reductase.

• Nucleotide analogs and inhibitors of nucleotide metabolism are used in drug therapy for diseases such as cancer, AIDS, herpes, etc.



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Nucleotides occur in mono-, di-, or triphosphate forms. Deoxyribonucleotides are present in DNA (deoxyribonucleic acid) only. Ribonucleotides are found in RNA (ribonucleic acid) and sometimes in DNA. Nucleosides are linked via a phosphodiester bridge in polynucleotides (RNA and DNA). The phosphodiester linkage occurs between the 5' and 3' carbons of the sugar ring.

Base Structures

B) NOMENCLATURE CONVENTIONS: [modified from Table 25-1]
 

C) RIBONUCLEOTIDE BIOSYNTHESIS: How are nucleotides for RNA made in cells?

PURINE NUCLEOTIDES

• The purine ring is synthesized from amino acids,tetrahydrofolate derivatives and C0₂ [Fig. 25-6]

• PRPP (phosphoribosylpyrophosphate) is the donor of the ribose phosphate unit upon which purine nucleotides are assembled. As with several other reactions we will study, the reaction with PRPP and glutamine (yielding 5-phosphoribosylamine and pyrophosphate) is the driving force for purine biosynthesis. Although thermodynamically reversible, the reaction is made irreversible as a result of breakdown of pyrophosphate (PPi) by pyrophosphatase. PRPP is also an important factor in the Nucleotide Salvage Pathways.

• IMP (inosine monophosphate) is the 1st purine nucleotide product of the biosynthetic pathway. IMP is the precursor of AMP and GMP. [Figs. 25-9] Feedback inhibition controls both the overall rate of purine biosynthesis and the balance between AMP and GMP production. [Fig. 25-16]

• Pyrimidine Biosynthesis The pyrimidine ring is synthesized first, then ribose phosphate is added from PRPP (another reaction rendered irreversible by pyrophosphatase)to form a pyrimidine nucleotide. UMP is the end product of pyrimidine pathway.
• CTP Biosynthesis CTP is formed from UTP by amination [pp. 694-698]

D) NUCLEOTIDE INTERCONVERSIONS:

Nucleoside mono (NMP), di (NDP), and tri (NTP)-phosphate interconvert by trading phosphate groups. These interconversions produce the activated NTPs and dNTPs which are substrates for nucleic acid synthesis. Some interconversions require ATP, some just exchange high energy phosphates.

PURINE SALVAGE: Two phosphribosyltransferase enzymes
    1) Adenine PPi 2Pi
    2) Hypoxanthine, guanine

DEOXYRIBONUCLEOTIDE SYNTHESIS

Reduction of ribonucleoside diphosphates by ribonucleotide reductase (using NADPH) yields the deoxyribonucleoside diphosphates (whose phosphorylation to dNTPs yields DNA precursors). The ribonucleotides must also be phosphorylated to the NTP level to provide the precursors for RNA synthesis.

• Ribonucleotide reductase is a multisubunit enzyme whose overall activity and specificity are regulated by nucleotides.

• Ribonucleotude reductase as a target for malaria drug treatment is the subject of a student project by Hillary Saxon.

DEOXYTHYMIDYLATE SYNTHESIS:
• The thymine-containing precursor of DNA is dTMP, which is synthesized after conversion of dUDP to dUMP. Thymidylate synthase catalyzes the synthesis of dTMP from dUMP by addition of a 5^'-CH₃ donated by N⁵, N¹⁰,-THFA. Two phosphorylations of dTMP are required to yield the dTTP precursor for DNA synthesis. [Fig. 25-13] Thymidylate synthase is a major target for anticancer therapy by: (a) competitive inhibition wit h folate analogs such as methotrexate or aminopterin[Figs. 25-14] or (b) suicide inhibitors such as 5-fluorouracil which, for example, is used in the treatment of actinic keratoses.

• DHFR Inhibitors, such as Methotrexate, can have varying sensitivities to different diseases.

• Cancer - one approach is use of inhibitors (ex: methotrexate) of nucleotide biosynthesis to stop growth of cancer cells by, ultimately, inhibiting DNA synthesis.

 
• AIDS treatment: Azidothymidine (AZT), a nucleotide analog which inhibits HIV reverse transcriptase.
  

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