STPM-Biological Molecules - Nucleic Acids

STPM-Biological Molecules - Nucleic Acids
This guide summarizes the provided text on nucleic acids, focusing on key concepts for improved understanding.
I. Nucleic Acid Fundamentals:

• Definition: Nucleic acids (DNA and RNA) are polynucleotides – biopolymers composed of nucleotides. They are the primary genetic material in all living organisms.

II. Nucleotide Structure and Composition:

• Components: Each nucleotide consists of three parts:
  • Nitrogenous Base: These are nitrogen-containing biochemicals.
    • Purines: Adenine (A) and Guanine (G) – two fused hydrocarbon rings.
    • Pyrimidines: Cytosine (C), Thymine (T) (DNA only), and Uracil (U) (RNA only) – one hydrocarbon ring. Refer to Figure 1.29 in the original text for visual representation.
  • Pentose Sugar: Either ribose (in RNA) or deoxyribose (in DNA).
  • Phosphate Group: Can be present as one, two, or three phosphate groups (monophosphate, diphosphate, triphosphate; e.g., AMP, ADP, ATP). These are water-soluble.
• Nucleotide Types:
  • Ribonucleotides: Contain ribose sugar, phosphate, and the bases A, C, G, and U (RNA).
  • Deoxyribonucleotides: Contain deoxyribose sugar, phosphate, and the bases A, C, G, and T (DNA).
• Key Bonds:
  • N-glycosidic bond: Connects the base to the sugar.
  • Phosphoester bond: Connects the sugar to the phosphate group.
• Hydrolysis:
  • Phosphatase/Nucleotidase: Hydrolyzes nucleotides into phosphate and nucleoside.
  • Nucleosidase: Hydrolyzes nucleosides into bases and pentoses.

III. Polynucleotide Formation (Polymerization):

• Phosphodiester Bond Formation: Nucleotides link together via condensation reactions, forming phosphodiester bonds between the 3'-hydroxyl (-OH) group of one nucleotide's sugar and the phosphate group of another. This creates a polynucleotide chain. Refer to Figure 1.30 in the original text for a visual of this condensation reaction.
• Types of Polynucleotides:
  • Deoxyribonucleic Acid (DNA): Replication (catalyzed by DNA polymerase) creates DNA.
  • Ribonucleic Acid (RNA): Transcription (catalyzed by RNA polymerase) creates RNA. (Detailed discussion in Chapter 3, per the original text.)
• Biological Significance: DNA and RNA synthesis is crucial for cell division (DNA) and protein synthesis (RNA). RNA synthesis, particularly mRNA, precedes polypeptide formation.

I. Nucleotides: The Building Blocks

• Structure: Nucleotides consist of three components (Fig 1.28):
  • Nitrogenous Base: These are either purines (Adenine (A) and Guanine (G) - two rings) or pyrimidines (Cytosine (C), Thymine (T) - DNA only, and Uracil (U) - RNA only - one ring) (Fig 1.29).
  • Pentose Sugar: Either ribose (RNA) or deoxyribose (DNA).
  • Phosphate Group(s): One to three phosphate groups can be attached, leading to nucleoside mono, di, or triphosphates (e.g., AMP, ADP, ATP). Remember examples like ATP, CTP, GTP, TTP, and UTP.
• Types:
  • Ribonucleotides: Contain ribose sugar and the bases A, C, G, and U; found in RNA.
  • Deoxyribonucleotides: Contain deoxyribose sugar and the bases A, C, G, and T; found in DNA.
• Bonding: The base and sugar are linked by an N-glycosidic bond. Nucleotides link together via phosphodiester bonds between the 3'-hydroxyl (-OH) group of one nucleotide's pentose sugar and the phosphate group of another, forming a polynucleotide chain. This is a condensation reaction.
• Hydrolysis: Phosphatases/nucleotidasess hydrolyze nucleotides into phosphates and nucleosides. Nucleosidases further break down nucleosides into bases and pentoses.

II. Polynucleotides: DNA and RNA

• Formation: Polynucleotides (DNA and RNA) are formed by polymerization of nucleotides through phosphodiester bond formation (condensation reaction). DNA synthesis (replication) is catalyzed by DNA polymerase, while RNA synthesis (transcription) is catalyzed by RNA polymerase. (Detailed in Chapter 3).
• DNA (Deoxyribonucleic Acid):
  • Structure (Watson-Crick Model): A double helix (Fig 1.31) with two antiparallel polynucleotide strands coiled around a common axis.
  • Bases: A, C, G, and T. A pairs with T (2 hydrogen bonds), and C pairs with G (3 hydrogen bonds).
  • Backbone: Deoxyribose and phosphate groups.
  • Stability: Hydrogen bonds between bases, hydrophobic interactions between bases in the center, and surrounding water molecules contribute to DNA's stability.
  • Dimensions: One complete turn of the helix is 3.4 nm long, containing 10 base pairs; diameter is 2 nm.
  • Location: Primarily in the nucleus.
• RNA (Ribonucleic Acid):
  • Structure: A single-stranded polynucleotide.
  • Bases: A, C, G, and U.
  • Backbone: Ribose and phosphate groups.
  • Types: Three main types with distinct roles:
    • rRNA (Ribosomal RNA): Forms the structural and catalytic core of ribosomes (80S in eukaryotes, 70S in prokaryotes). It comprises about 80% of cellular RNA. It has a catalytic role as a ribozyme, forming peptide bonds.
    • tRNA (Transfer RNA): Cloverleaf structure (Fig 1.32), carries specific amino acids to the ribosome during translation. It contains an anticodon that base-pairs with mRNA codons. Makes up about 10-15% of cellular RNA.
    • mRNA (Messenger RNA): Carries genetic information from DNA to the ribosome for protein synthesis. Its sequence is complementary to the DNA template strand and identical (except for U replacing T) to the coding strand. It is relatively short-lived. Makes up about 5% of cellular RNA.

I. DNA Structure: The Double Helix
A. Fundamental Components:

• Double-stranded helix: Two polynucleotide chains intertwine around a common axis (Watson-Crick model). Visualize this as a twisted ladder.
• Deoxyribonucleotides: Building blocks composed of:
  • Deoxyribose sugar: A 5-carbon sugar lacking an oxygen atom compared to ribose (RNA).
  • Phosphate group: Forms the backbone through phosphodiester bonds.
  • Nitrogenous bases: Adenine (A), Cytosine (C), Guanine (G), Thymine (T).
• Base Pairing: Specific hydrogen bonding between bases:
  • A pairs with T (2 hydrogen bonds)
  • C pairs with G (3 hydrogen bonds) This is complementary base pairing.
• Antiparallel strands: The two strands run in opposite directions (5' to 3' and 3' to 5'). Think of the ladder rungs being upside down relative to each other.
• Dimensions:
  • One complete turn of the helix: 3.4 nm (10 base pairs)
  • Diameter of the helix: 2 nm
• Stability: Hydrogen bonds between bases, hydrophobic interactions within the core of the helix (bases), and surrounding water molecules contribute to the stability of the DNA structure.

B. Key Points for Memorization:

• Think "AT" and "GC": This helps remember the base pairing rules.
• "Deoxy"ribose lacks an oxygen: Distinguish DNA from RNA.
• Antiparallel: Imagine the 5' and 3' ends pointing in opposite directions.

II. RNA Structure: The Single-Stranded Variations
A. General Features:

• Single-stranded polynucleotide: Unlike DNA, RNA is typically a single-stranded molecule.
• Ribose sugar: Contains an extra oxygen atom compared to deoxyribose.
• Nitrogenous bases: Adenine (A), Cytosine (C), Guanine (G), Uracil (U) – note the absence of Thymine and presence of Uracil.
• Three main types: rRNA, tRNA, mRNA. Each plays a crucial role in protein synthesis.

B. Types of RNA:

1. Ribosomal RNA (rRNA):
   • Abundance: ~80% of cellular RNA.
   • Lifespan: Several days.
   • Structure: Combines intra-chain single-stranded and double-stranded sections bound to proteins to form ribosomes.
   • Ribosome Subunits: Eukaryotes (80S = 60S + 40S); Prokaryotes (70S = 50S + 30S). The numbers represent sedimentation coefficients, not actual sizes.
   • Function: Forms the ribosome, the site of protein synthesis. Recent research suggests it also functions as a ribozyme (catalytic RNA).
   • Location of synthesis: Nucleolus (eukaryotes).
   • Key Point: Remember the ribosomal subunit sizes for eukaryotes and prokaryotes.
2. Transfer RNA (tRNA):
   • Abundance: 10-15% of cellular RNA.
   • Lifespan: Several hours.
   • Structure: Cloverleaf shape due to intra-chain hydrogen bonding.
   • Size: Smallest type of RNA (~80 nucleotides).
   • Types: 61 types (one for each codon except stop codons).
   • Anticodon: A three-base sequence that complements a specific mRNA codon.
   • Amino acid attachment site (CCA): At the 3' end, it binds a specific amino acid.
   • Function: Carries amino acids to the ribosome for protein synthesis.
   • Key Point: The anticodon is crucial for matching the tRNA to the correct mRNA codon.
3. Messenger RNA (mRNA):
   • Abundance: ~5% of cellular RNA.
   • Lifespan: Shortest lifespan (minutes).
   • Structure: Linear; can be long (several genes can be transcribed into one mRNA) and may coil or fold.
   • Function: Carries genetic information from DNA to the ribosome, acting as a template for protein synthesis.
   • Key Point: mRNA is a temporary carrier of genetic information.

DNA vs. RNA: A Comparative Study Guide
This guide summarizes the key differences between DNA (Deoxyribonucleic Acid) and RNA (Ribonucleic Acid), crucial for understanding their distinct roles in cellular processes.

Understanding the Significance of Differences
The differences highlighted above are not arbitrary; they directly impact the function of each molecule:

• Structure and Size: DNA's double helix provides stability for long-term storage of genetic information, while RNA's single strand allows for greater flexibility and transient interactions needed for protein synthesis.
• Base Composition: The substitution of Uracil for Thymine is functionally relevant, as Uracil is more easily generated within the cell, and its incorporation influences the interaction of RNA with DNA.
• Location and Amount: DNA's primarily nuclear location reflects its role as the repository of genetic information. RNA's presence in both nucleus and cytoplasm emphasizes its diverse roles in transcription and translation (protein synthesis).
• Stability: DNA's stability ensures the integrity of the genetic code across generations, while RNA's instability ensures it is only present when needed for protein synthesis.
• Types of RNA: The three major types of RNA, each with specific roles, highlight the multifunctional nature of RNA in the central dogma of molecular biology:
  • mRNA (messenger RNA): Carries genetic information from DNA to the ribosomes.
  • tRNA (transfer RNA): Transports amino acids to the ribosomes during translation.
  • rRNA (ribosomal RNA): A structural component of ribosomes, crucial for protein synthesis.