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Biochemistry-II - Purines and Pyrimidines

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    Study Guide Biochemistry - II – Purines and Pyrimidines 1. Purine and Pyrimidine Structures Introduction to Nitrogenous Bases DNA and RNA are made from small building blocks called nitrogenous bases . These bases are divided into two main groups: pyrimidines and purines . Even though they are both essential for nucleic acids, their structures and metabolic pathways are different. Pyrimidine Bases Pyrimidines have a single, six - membered ring . This ring contains four carbon atoms and two nitrogen atoms . The three main pyrimidine bases are: • Cytosine • Thymine • Uracil Each of these bases has a slightly different arrangement of atoms, but all share the same basic ring structure.

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    Study Guide Purine Bases Purines are larger than pyrimidines. They have a double - ring structure made up of: • One six - membered ring • One five - membered ring Together, purines contain nine atoms , including five carbons and four nitrogens .

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    Study Guide The two main purine bases are: • Adenine • Guanine These bases are essential components of DNA and RNA. Key Differences Between Purines and Pyrimidines Although both purines and pyrimidines include a six - membered ring with nitrogen atoms, they are not metabolically related . This means: • Purine biosynthesis and degradation follow separate pathways • Pyrimidine biosynthesis and degradation follow different pathways These distinct pathways are found in all living organisms .

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    Study Guide Nucleosides and Nucleotides What Is a Nucleoside? When a five - membered sugar (carbohydrate) ring combines with a purine or pyrimidine base , the molecule is called a nucleoside . Important points: • The atoms in the base are numbered normally. • The sugar carbons are numbered using a prime (′) symbol (for example, 1′, 2′, 3′). • This helps distinguish sugar atoms from base atoms. Examples of nucleosides include: • Deoxyguanosine • 2′ - O - methyladenosine What Is a Nucleotide? If one or more phosphate groups are added to a nucleoside, the molecule becomes a nucleotide . For example: • 3′ - cytidine monophosphate is a nucleotide • ATP (adenosine triphosphate) is also a nucleotide and plays a major role in energy transfer in cells

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    Study Guide Key Takeaways • Pyrimidines : single six - membered ring (Cytosine, Thymine, Uracil) • Purines : double - ring structure (Adenine, Guanine) • Nucleoside = base + sugar • Nucleotide = nucleoside + phosphate • Purines and pyrimidines have separate metabolic pathways 2. Salvage and Biosynthetic Pathways of Nucleotides Overview: How Cells Get Nucleotides Cells need a constant supply of nucleotides and nucleosides . These molecules are essential for: • Making DNA and RNA • Acting as energy carriers (like ATP) • Serving as signaling molecules • Forming parts of important cellular compounds Cells can obtain nucleotides in three main ways : 1. Salvage pathways – recycling existing bases 2. Biosynthesis (de novo synthesis) – building nucleotides from small precursors

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    Study Guide 3. Degradation pathways – breaking down excess nucleotides These three pathways are closely connected and work together to maintain balance in the cell. Why Balance Is So Important Nucleotide balance is critical for normal cell function. • DNA requires equal amounts of A and T , and equal amounts of C and G • RNA also needs balanced nucleotide levels • Too few nucleotides → DNA and RNA synthesis slows or stops • Too many nucleotides → toxic effects, especially from purines Because purines and purine nucleosides can be toxic to humans, excess purines must be safely removed . Salvage Pathways: Recycling Nucleotides Constant Turnover in the Cell Inside cells, DNA and RNA are constantly being: • Synthesized • Repaired • Broken down During DNA repair, parts of DNA are temporarily broken into: • Free bases • Nucleosides • Nucleotides Instead of wasting these components, cells recycle them using salvage pathways . Role of PRPP in Salvage A key molecule in salvage pathways is phosphoribosyl pyrophosphate (PRPP) .

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    Study Guide • PRPP is made from ribose - 5 - phosphate • Ribose - 5 - phosphate comes from the pentose phosphate pathway • PRPP acts as an activated ribose donor PRPP is not only important for nucleotide metabolism but also activates other nitrogen - containing biosynthetic pathways. Figure 1

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    Study Guide Salvage Enzymes Different enzymes recycle different bases: • One enzyme salvages guanine or hypoxanthine • A second enzyme salvages adenine • A third enzyme is specific for uracil and thymine All these enzymes perform the same basic reaction: • They transfer a free base to PRPP • The product is a nucleoside - 5′ - monophosphate (NMP) Purine Biosynthesis (De Novo Pathway) General Strategy In purine biosynthesis: • The ribose - phosphate backbone (from PRPP) is formed first • The purine ring is built step by step on this backbone The final product of this pathway is inosine monophosphate (IMP) .

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    Study Guide First Step: Formation of PRA The first committed step is: • Transfer of an amide group from glutamine to PRPP • Pyrophosphate is released • The product is phosphoribosylamine (PRA) Building the Purine Ring (Step - by - Step) 1. Glycine is added to PRA → forms glycinamide ribonucleotide 2. The amino group of glycine is formylated o Formyl group comes from N¹⁰ - formyltetrahydrofolate

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