Chemistry of Nucleotides & Nucleic Acids

Purines & Pyrimidine Bases

• Purines and pyrimidines are types of nitrogenous bases found in the structure of nucleotides, the building blocks of nucleic acids like DNA and RNA.
• These bases are essential for encoding genetic information and forming the base pairs that hold the two strands of DNA together.

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1. Purines

Structure:

• Purines are double-ringed structures consisting of a six-membered ring fused to a five-membered ring. This structure makes purines larger and more complex compared to pyrimidines.

Examples of Purines:

1. Adenine (A):

   • Found in both DNA and RNA.

   • Pairs with Thymine (T) in DNA and Uracil (U) in RNA.

2. Guanine (G):

   • Found in both DNA and RNA.

   • Pairs with Cytosine (C) in both DNA and RNA.

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Functions:

• Purines, specifically Adenine and Guanine, play critical roles in the structure and function of nucleic acids. They form part of the genetic code by pairing with pyrimidines to create complementary base pairs. This pairing is vital for the structure and stability of DNA and RNA.

• Purines also play a significant role in energy transfer. The purine nucleotide ATP (Adenosine Triphosphate) is a key energy carrier in cells.

• Some coenzymes like NAD+ (Nicotinamide adenine dinucleotide) and FAD (Flavin adenine dinucleotide) are derived from purines and are involved in crucial metabolic pathways.

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2. Pyrimidines

Structure:

• Pyrimidines have a single-ring structure, consisting of a six-membered ring. This makes pyrimidines smaller in size compared to purines.

Examples of Pyrimidines:

1. Cytosine (C):

   • Found in both DNA and RNA.

   • Pairs with Guanine (G) in both DNA and RNA.

2. Thymine (T):

   • Found only in DNA.

   • Pairs with Adenine (A) in DNA.

3. Uracil (U):

   • Found only in RNA.

   • Replaces Thymine (T) in RNA and pairs with Adenine (A) in RNA.

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Functions:

• Pyrimidines, like Cytosine, Thymine, and Uracil, are responsible for forming the complementary base pairs with purines in DNA and RNA.

• Cytosine pairs with Guanine in both DNA and RNA, while Thymine pairs with Adenine in DNA, and Uracil pairs with Adenine in RNA. This base-pairing mechanism ensures that the genetic code is faithfully copied and transcribed.

• Pyrimidines are involved in various biological processes such as gene expression, DNA replication, and RNA synthesis. Their involvement in the synthesis of nucleic acids is essential for cell division, protein synthesis, and other cellular functions.

 

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Nucleotides

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Structure of Nucleotides:

A nucleotide is composed of three main components:

1. Nitrogenous Base: A purine or pyrimidine base that carries genetic information.

2. Pentose Sugar: A five-carbon sugar, which can either be ribose (in RNA) or deoxyribose (in DNA).

3. Phosphate Group(s): One or more phosphate groups attached to the 5’ carbon of the sugar. Nucleotides can be monophosphate, diphosphate, or triphosphate (e.g., ATP, ADP, AMP).

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Types of Nucleotides:

• Ribonucleotides: These nucleotides are the building blocks of RNA (ribonucleic acid). The sugar is ribose, and the nitrogenous bases are adenine (A), guanine (G), cytosine (C), and uracil (U).

  • ATP (Adenosine triphosphate): Energy carrier.

  • GTP (Guanosine triphosphate): Involved in protein synthesis and cellular signaling.

  • CTP (Cytidine triphosphate): Involved in lipid synthesis.

  • UTP (Uridine triphosphate): Involved in the synthesis of RNA and glycogen metabolism.

• Deoxyribonucleotides: These nucleotides are the building blocks of DNA (deoxyribonucleic acid). The sugar is deoxyribose, and the nitrogenous bases are adenine (A), guanine (G), cytosine (C), and thymine (T).

  • dATP (Deoxyadenosine triphosphate): Used in DNA synthesis.

  • dGTP (Deoxyguanosine triphosphate): Used in DNA synthesis.

  • dCTP (Deoxycytidine triphosphate): Used in DNA synthesis.

  • dTTP (Deoxythymidine triphosphate): Used in DNA synthesis.

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Functions of Nucleotides:

1. Genetic Information Storage: The sequence of nucleotides in DNA and RNA encodes genetic instructions that direct cellular activities, including protein synthesis and cell division.

2. Energy Transfer: Nucleotides like ATP (Adenosine triphosphate) are crucial in energy transfer. ATP, for instance, is used as an energy currency in the cell to drive processes like muscle contraction, protein synthesis, and active transport across membranes.

3. Coenzymes: Many coenzymes, such as NAD+ (Nicotinamide adenine dinucleotide) and FAD (Flavin adenine dinucleotide), are derived from nucleotides. These molecules assist enzymes in catalyzing biochemical reactions, especially in cellular respiration.

4. Signaling: Nucleotides also play a significant role in cell signaling. For instance, cAMP (Cyclic AMP) and cGMP (Cyclic GMP) are secondary messengers involved in regulating various cellular processes like hormone release, neurotransmitter signaling, and immune response.

 

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Nucleosides

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Structure of Nucleosides:

A nucleoside is similar to a nucleotide, but it lacks the phosphate group. It consists of:

1. Nitrogenous Base: Either a purine (adenine, guanine) or pyrimidine (cytosine, thymine, uracil).

2. Pentose Sugar: A five-carbon sugar, which can be ribose (in RNA) or deoxyribose (in DNA).

The absence of the phosphate group distinguishes nucleosides from nucleotides.

Examples of Nucleosides:

1. Adenosine: Adenine + ribose.

2. Guanosine: Guanine + ribose.

3. Cytidine: Cytosine + ribose.

4. Thymidine: Thymine + deoxyribose.

5. Uridine: Uracil + ribose.

Nucleosides vs Nucleotides:

• A nucleotide has three components: a nitrogenous base, a sugar, and one or more phosphate groups.

• A nucleoside consists of only two components: a nitrogenous base and a sugar.

• Nucleosides are precursors to nucleotides, and phosphorylation of nucleosides (i.e., the addition of phosphate groups) converts them into nucleotides.

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Functions of Nucleosides:

• Nucleosides can be converted into nucleotides by the addition of one or more phosphate groups, forming nucleotides that play essential roles in cellular processes like DNA and RNA synthesis.

• Adenosine (a nucleoside) can be converted into ATP (a nucleotide) to participate in energy transfer within the cell.

• Some nucleosides have pharmacological applications.

• For example, Adenosine has been used in the treatment of arrhythmias, and some nucleoside analogs are used as antiviral or anticancer drugs.

 

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Difference Between Nucleotides and Nucleosides

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DNA (Deoxyribonucleic Acid)

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• DNA is a long molecule that carries the genetic instructions used in the growth, development, functioning, and reproduction of all living organisms.
• It is often described as the blueprint for life because it contains the information needed to build and maintain the organism.

Structure of DNA

• The structure of DNA was first described by James Watson and Francis Crick in 1953, with significant contributions from Rosalind Franklin and Maurice Wilkins.
• Their discovery revealed the double-helix structure of DNA, which is fundamental for its function.

Key Components of DNA Structure:

1. Double-Helix Structure:

   • DNA is composed of two polynucleotide strands that twist around each other, forming a double helix. The two strands run in opposite directions, meaning they are antiparallel.

2. Nucleotides:

   • Each strand of DNA is made up of subunits called nucleotides. Each nucleotide consists of:

     • A phosphate group.

     • A deoxyribose sugar (a five-carbon sugar).

     • A nitrogenous base (one of four types: adenine (A), thymine (T), cytosine (C), and guanine (G)).

3. Base Pairing:

   • The two strands of DNA are connected by hydrogen bonds between complementary nitrogenous bases. The bases pair in a specific way:

     • Adenine (A) pairs with Thymine (T).

     • Cytosine (C) pairs with Guanine (G).

   • These base pairs form the “rungs” of the DNA ladder, while the sugar-phosphate backbone forms the “sides” of the ladder.

4. Antiparallel Strands:

   • The two strands of DNA run in opposite directions. One strand runs from the 5′ (5-prime) end to the 3′ (3-prime) end, while the complementary strand runs in the opposite direction.

5. Helical Twist:

   • The structure twists into a right-handed double helix, with about 10 base pairs per complete turn.

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Types of DNA

• Chromosomal DNA:

  • In eukaryotic cells, DNA is found inside the nucleus and is packaged into structures called chromosomes.

  • In prokaryotes (such as bacteria), DNA is typically found in a single, circular chromosome located in the nucleoid region of the cell.

• Mitochondrial DNA:

  • In eukaryotic cells, DNA is also present in the mitochondria (the energy-producing organelles), and this DNA is inherited maternally.

• Plasmid DNA:

  • Small, circular pieces of DNA found in bacteria and other microorganisms, often containing genes that confer advantages, such as antibiotic resistance.

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Functions of DNA

DNA plays a central role in the storage and transmission of genetic information. Its functions include:

1. Genetic Information Storage:

   • DNA stores all the information necessary for an organism’s development, functioning, and reproduction.

   • This information is encoded in the sequence of nitrogenous bases (A, T, C, and G).

2. Replication:

   • Before a cell divides, DNA must be replicated so that both daughter cells receive an identical copy of the genetic material.

   • The process of DNA replication is semi-conservative, meaning that each new DNA molecule consists of one old (template) strand and one newly synthesized strand.

3. Protein Synthesis:

   • DNA provides the instructions for protein synthesis through two major processes:

     1. Transcription: The DNA sequence is transcribed into a messenger RNA (mRNA) molecule.

     2. Translation: The mRNA is translated into a specific protein sequence on the ribosome, using the genetic code.

4. Regulation of Cellular Activities:

   • Specific genes in DNA regulate various cellular processes, such as cell growth, division, and response to environmental signals.

   • Gene expression is tightly controlled to ensure proper function and homeostasis of the cell.

5. Inheritance:

   • DNA is passed from one generation to the next during reproduction, ensuring the continuity of genetic traits.

   • This is a key element of the theory of inheritance and genetic evolution.

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Differences Between DNA and RNA

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RNA (Ribonucleic Acid)

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• RNA (Ribonucleic Acid) is a crucial molecule in the biological processes of living organisms, acting as a template for protein synthesis and playing vital roles in gene expression and regulation.
• While DNA is the genetic blueprint for organisms, RNA is involved in translating that genetic information into functional proteins and regulating cellular activities.

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Structure of RNA

RNA is structurally similar to DNA, with some key differences that make it unique. Here’s a detailed breakdown of its structure:

Components of RNA:

1. Ribose Sugar:

   • RNA contains ribose as the sugar component, which is a five-carbon sugar with a hydroxyl group (-OH) attached to the 2′ carbon. In contrast, DNA uses deoxyribose, which has a hydrogen atom instead of a hydroxyl group on the 2′ carbon.

2. Nitrogenous Bases:

   • RNA has four nitrogenous bases, similar to DNA, but with one major difference:

     • Adenine (A)

     • Guanine (G)

     • Cytosine (C)

     • Uracil (U) (instead of thymine, which is found in DNA).

3. Phosphate Group:

   • Like DNA, RNA contains a phosphate backbone. This backbone is formed by alternating phosphate and ribose molecules, linking the nitrogenous bases together.

RNA vs DNA Structural Differences:

• Single-Stranded: RNA typically exists as a single strand, unlike DNA, which is double-stranded and forms a double helix. This single-stranded nature allows RNA to be more flexible and able to adopt various functional forms.

• Uracil vs Thymine: Instead of thymine (T), RNA contains Uracil (U), which pairs with Adenine (A) during processes like transcription.

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Types of RNA

There are several types of RNA, each with specific functions in the cell. These include:

1. Messenger RNA (mRNA):

• Function: mRNA is a template that carries the genetic code from the DNA to the ribosomes, where proteins are synthesized. It is transcribed from the DNA in the nucleus and then travels to the cytoplasm for translation.

• Structure: mRNA is a single-stranded molecule that reflects the genetic code of a gene. The sequence of nucleotides in mRNA determines the sequence of amino acids in a protein.

2. Transfer RNA (tRNA):

• Function: tRNA plays a critical role in protein synthesis by transferring specific amino acids to the ribosome, where proteins are assembled. Each tRNA molecule has an anticodon region that recognizes and binds to the corresponding codon on the mRNA.

• Structure: tRNA has a characteristic cloverleaf shape due to its extensive base pairing. One part of the molecule attaches to an amino acid, and the opposite end has an anticodon that pairs with the mRNA codon.

3. Ribosomal RNA (rRNA):

• Function: rRNA forms a significant part of the ribosomes, which are the cellular machinery responsible for protein synthesis. rRNA catalyzes the formation of peptide bonds between amino acids.

• Structure: rRNA is structurally associated with proteins to form the ribosome’s large and small subunits.

4. Small Nuclear RNA (snRNA):

• Function: snRNA is involved in the splicing of pre-mRNA in eukaryotic cells, a process that removes introns (non-coding regions) and joins exons (coding regions) together to form mature mRNA.

• Structure: snRNA is typically a small, non-coding RNA that associates with proteins to form small nuclear ribonucleoproteins (snRNPs).

5. MicroRNA (miRNA) and Small Interfering RNA (siRNA):

• Function: These small RNA molecules are involved in RNA silencing and post-transcriptional regulation of gene expression. They bind to complementary mRNA sequences, leading to the degradation or inhibition of translation.

• Structure: Both miRNA and siRNA are short RNA molecules (approximately 20-25 nucleotides) that regulate gene expression at the level of translation.

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Functions of RNA

RNA is essential for the flow of genetic information within the cell, and its functions include:

1. Protein Synthesis (Translation):

RNA is critical in translating genetic information into proteins. The process involves:

• mRNA: Carries the genetic code from the DNA to the ribosome, where proteins are synthesized.

• tRNA: Brings the appropriate amino acids to the ribosome, matching its anticodon with the codons on the mRNA.

• rRNA: Forms the core of the ribosome, catalyzing the assembly of amino acids into polypeptides and facilitating protein synthesis.

2. Gene Regulation:

• RNA molecules, such as miRNA and siRNA, regulate gene expression at the post-transcriptional level.
• They can either degrade or inhibit the translation of mRNA, thus controlling which proteins are produced.

3. Splicing of Pre-mRNA:

• In eukaryotic cells, snRNA helps in the splicing of pre-mRNA, removing non-coding regions (introns) and joining the coding regions (exons).
• This process ensures that only the functional parts of the gene are included in the mature mRNA.

4. Catalysis:

• Some RNA molecules have enzymatic activity and can catalyze chemical reactions.
• These are called ribozymes. For example, rRNA in the ribosome catalyzes the formation of peptide bonds during protein synthesis.