4. Nucleotides, Nucleic Acids, and Genetic Information

4.1 Nucleotides

Nucleotides are the fundamental building blocks of nucleic acids, such as DNA and RNA. Each nucleotide consists of three components: a nitrogenous base, a five-carbon sugar (ribose in RNA, deoxyribose in DNA), and one or more phosphate groups.

• Nitrogenous bases: Purines (adenine, guanine) and pyrimidines (cytosine, thymine in DNA; uracil in RNA).

• Sugar: Deoxyribose in DNA, ribose in RNA.

• Phosphate group: Links nucleotides together via phosphodiester bonds.

Example: ATP (adenosine triphosphate) is a nucleotide that serves as an energy carrier in cells.

4.2 Nucleic Acid Structure

Nucleic acids are polymers of nucleotides linked by phosphodiester bonds. DNA is typically double-stranded, forming a double helix, while RNA is usually single-stranded but can form complex secondary structures.

• DNA Structure: Double helix with antiparallel strands (5' to 3' and 3' to 5').

• Base pairing: Adenine (A) pairs with Thymine (T) via two hydrogen bonds; Guanine (G) pairs with Cytosine (C) via three hydrogen bonds.

• Complementarity: Each strand serves as a template for the other. For example, the sense strand 5'-GACGGTAATGAC-3' pairs with the antisense strand 3'-CTGCCATT ACTG-5'.

• RNA Structure: Single-stranded, contains ribose sugar, and uracil (U) replaces thymine (T). RNA can form stem-loop structures due to intramolecular base pairing.

Example: The structure of tRNA includes stem-loops formed by complementary base pairing within the same strand.

4.3 Nucleic Acid Function

DNA and RNA play central roles in the storage, transmission, and expression of genetic information.

• DNA: Stores genetic information, undergoes replication, and serves as a template for transcription.

• RNA: Functions in gene expression (mRNA, tRNA, rRNA) and can also have catalytic roles (ribozymes).

Example: mRNA carries the genetic code from DNA to ribosomes for protein synthesis.

4.4 DNA Replication

DNA replication is the process by which a cell duplicates its DNA before cell division. The double-stranded nature of DNA allows each strand to serve as a template for the synthesis of a new complementary strand.

• Key enzymes:

  • DNA helicase: Unwinds the DNA double helix.

  • DNA ligase: Seals gaps between Okazaki fragments on the lagging strand.

  • Topoisomerase: Relieves supercoiling ahead of the replication fork.

  • DNA polymerase: Adds nucleotides (dNTPs) to the growing DNA strand.

• Semiconservative replication: Each new DNA molecule consists of one parental and one daughter strand.

Equation:

4.5 Polymerase Chain Reaction (PCR)

PCR is a laboratory technique used to amplify specific DNA sequences exponentially without the need for living cells.

• Components: DNA template, primers, dNTPs, Taq polymerase.

• Steps:

  1. Denaturation (94°C): DNA strands separate.

  2. Annealing (55°C): Primers bind to target sequences.

  3. Extension (70°C): Taq polymerase synthesizes new DNA strands.

  This cycle is repeated 35-40 times for exponential amplification.

Example: PCR is used in genetic testing, forensic analysis, and molecular biology research.

4.6 Transcription and Translation

The central dogma of molecular biology describes the flow of genetic information from DNA to RNA to protein.

• Transcription: DNA is transcribed to produce a complementary RNA molecule (mRNA).

• Translation: mRNA is translated into a sequence of amino acids to form a protein.

• Key RNA types:

  • mRNA (messenger RNA): Encodes protein sequences.

  • tRNA (transfer RNA): Brings amino acids to the ribosome during translation.

  • rRNA (ribosomal RNA): Structural and catalytic component of ribosomes.

Equation:

4.7 Genetic Mutations and Disease

Mutations are changes in the genetic material that can alter protein structure and function. Some mutations are harmless, while others can cause diseases.

• Sickle Cell Anemia: Caused by a single nucleotide mutation in the β-globin gene, resulting in abnormal hemoglobin (Glu → Val substitution).

• Single-nucleotide polymorphisms (SNPs): Variations at a single nucleotide position in the genome, present in >1% of the population. Some SNPs are associated with increased risk for diseases such as cancer and type 2 diabetes.

Example: The mutation causing sickle cell anemia changes the codon GAG (glutamate) to GTG (valine) in the DNA sequence.

4.8 Nucleic Acid Sequencing

Nucleic acid sequencing determines the precise order of nucleotides in a DNA or RNA molecule.

• Nucleic acid sequence: The succession of letters (A, T/U, G, C) representing the order of nucleotides.

• Sequencing direction: Sequences are always presented from the 5' end to the 3' end.

• Applications: Genome sequencing, mutation detection, evolutionary studies.

Table: Comparison of DNA and RNA

Additional info: This summary integrates and expands upon the provided lecture slides and notes, ensuring a comprehensive, self-contained study guide for biochemistry students.