Ch3: Nucleic Acid Structure and Function

Section 3.1: 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 pentose sugar, and one or more phosphate groups.

• Nitrogenous Bases:

  • Purines: Adenine (A) and Guanine (G) have a double-ring structure.

  • Pyrimidines: Cytosine (C), Thymine (T, found in DNA), and Uracil (U, found in RNA) have a single-ring structure.

• Pentose Sugars:

  • Ribose: Found in RNA, contains a 2'-OH group.

  • Deoxyribose: Found in DNA, lacks a 2'-OH group.

• Phosphate Groups:

  • Usually attached to the 5' carbon of the sugar.

  • Can be present as mono-, di-, or triphosphates (e.g., AMP, ADP, ATP).

• Nucleoside vs. Nucleotide:

  • Nucleoside: Base + sugar

  • Nucleotide: Base + sugar + phosphate

Table: Nucleoside and Nucleotide Nomenclature

• Nucleotide Derivatives:

  • Coenzyme A, NAD, and FAD contain adenosine and play roles in metabolism and redox reactions.

Section 3.2: Nucleic Acid Structure

DNA and RNA are polymers of nucleotides linked by phosphodiester bonds. Their structures and physical properties are essential for their biological functions.

• Phosphodiester Bonds: Link the 3' carbon of one sugar to the 5' carbon of the next via a phosphate group.

• Base Pairing:

  • Adenine pairs with Thymine (A-T) via 2 hydrogen bonds.

  • Guanine pairs with Cytosine (G-C) via 3 hydrogen bonds.

• Double Helix:

  • DNA forms a right-handed double helix with antiparallel strands.

  • Major and minor grooves are formed by the twisting of the helix.

• Stabilizing Forces:

  • Base stacking interactions (hydrophobic and van der Waals forces) are the primary stabilizing force.

  • Hydrogen bonding between base pairs also contributes to stability.

• Factors Affecting Stability:

  • Water molecules stabilize the helix.

  • AT-rich regions are less stable than GC-rich regions due to fewer hydrogen bonds and lower stacking energy.

• RNA Structure:

  • RNA is typically single-stranded but can form complex secondary structures (e.g., tRNA).

  • RNA contains uracil instead of thymine.

• Denaturation and Renaturation:

  • DNA can denature (unfold) upon heating; the melting temperature () is the midpoint of the melting curve.

  • Renaturation (annealing) occurs when complementary strands reassociate at lower temperatures.

Section 3.3: The Central Dogma

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

• Replication: DNA is copied to produce identical molecules for cell division.

• Transcription: DNA is transcribed into RNA. The RNA transcript is complementary to the DNA template strand.

• Translation: RNA is translated into protein at the ribosome, using the genetic code to specify amino acids.

• Reverse Transcription: In some cases (e.g., retroviruses), RNA can be reverse-transcribed into DNA.

Types of RNA

• Messenger RNA (mRNA): Encodes polypeptide sequences.

• Transfer RNA (tRNA): Carries amino acids to the ribosome.

• Ribosomal RNA (rRNA): Forms the core of the ribosome and catalyzes protein synthesis.

• Other RNAs: ncRNA, snRNA, snoRNA, miRNA, siRNA, piRNA, etc.

Genetic Code Table

• Redundancy: Multiple codons can encode the same amino acid.

• Mutations: Changes in DNA sequence can alter protein structure and function, leading to diseases such as sickle cell anemia (E6V mutation in beta globin gene).

Section 3.4: Genomics

Genomics is the study of the structure, function, evolution, and mapping of genomes. It provides insights into gene identification, organismal complexity, and disease associations.

• Gene Identification: Techniques such as sequencing and comparative genomics are used to identify genes.

• Genome Complexity: Gene number and size are roughly correlated with organismal complexity.

• Model Organisms:

  • Escherichia coli, Saccharomyces cerevisiae, Caenorhabditis elegans, Arabidopsis thaliana

• Human Genome:

  • Only about 1.5% codes for proteins; the rest includes regulatory and repetitive sequences.

  • Coding and noncoding regions have distinct functions.

• Functional Classification: Genes are grouped by biochemical function (e.g., immune response, metabolism).

• Genomic Variation and Disease:

  • Single-nucleotide polymorphisms (SNPs) are used to study genetic predisposition to diseases.

  • Genome-wide association studies (GWAS) identify correlations between genetic variants and diseases.

Table: Coding and Noncoding Genome Portions

Review Questions

• Practice drawing the structures of purine and pyrimidine bases, ribose, and deoxyribose.

• Sketch the overall structure of a nucleoside and a nucleotide.

• Explain how Chargaff’s rules helped reveal the structure of DNA.

• Describe the arrangement of base pairs and sugar-phosphate backbones in DNA.

• List the ways that RNA differs from DNA.

• Describe the molecular events in DNA denaturation and renaturation.

• Draw a diagram to illustrate each step of the central dogma.

• Practice locating the codons for each of the 20 amino acids.

• Explain the relationship between mutations and disease.

• Describe the usefulness of identifying genetic variations between individuals.

• Explain the value and limitations of genome-wide association studies.

• List some positive and negative outcomes of gene therapy.

• Describe the approaches used to identify genes.

• Outline the correlation between gene number and organismal lifestyle.

• List some ways in which the human genome differs from a bacterial genome.

• List some practical applications of genomics.

Additional info: These notes expand on the provided slides and images, adding definitions, examples, and tables for clarity and completeness.