Nucleotides, DNA vs RNA, and Energy Carriers

Nucleotides have five-carbon sugars; two main types in biology: deoxyribose (DNA) and ribose (RNA).
Key structural difference at the 2' position:
- If the 2' position bears an OH group, the sugar is ribose → RNA.
- If the 2' position bears only a hydrogen (no OH), the sugar is deoxyribose → DNA.
- This difference is often remembered with the name deoxyribose (deoxygenated at the 2' position).
Visual cue from models: the 5 carbons form the sugar ring, with the 2' carbon chemistry distinguishing RNA from DNA.
Summary: RNA contains ribose with $2^{\prime}\text{-OH}$ ; DNA contains deoxyribose with $2^{\prime}\text{-H}$ .

Two categories of bases attached to the sugar:
- Purines: $\text{A}, \text{G}$ (double-ring structures).
- Pyrimidines: $\text{C}, \text{T}, \text{U}$ (single-ring structures).
Size relationship: Purines are larger (double-ring) than pyrimidines (single-ring).
In the DNA model: four colors represent the four bases; purines are larger, pyrimidines smaller, reflecting the size difference.
Base letters commonly used: A, G, C, T (DNA) or U (RNA).
Summary: Purines = ${\text{A}, \text{G}}$ ; Pyrimidines = ${\text{C}, \text{T}, \text{U}}$ .

Backbone composition: alternating sugar and phosphate units forming the backbone of DNA.
Sugar–phosphate backbone: connected by covalent bonds known as phosphodiester bonds (strong, not prone to breakdown over time).
- Representation: [sugar]–(phosphate)–[sugar]–(phosphate)–…
Bases protrude from the backbone and pair in the center of the molecule.
Double helix: two backbones twist around each other, forming a spiral structure.
Base pairing in the center:
- DNA base pairs are: $\text{A} \leftrightarrow \text{T}$ and $\text{C} \leftrightarrow \text{G}$ .
- Each pair consists of a purine–pyrimidine combination (A with T, C with G).
The sequence of bases encodes genetic information used to add amino acids to proteins.
Bond types:
- Backbone bonds: phosphodiester bonds (covalent, strong).
- Base pairing: hydrogen bonds (weak, enabling strand separation during replication and transcription).
Practical implication: the weak hydrogen bonds allow the two strands to be separated when needed, while the covalent backbone maintains integrity overall.

RNA sugar: ribose (not deoxyribose), shown earlier as the sugar in ribonucleotides.
Bases in RNA: includes uracil (U) instead of thymine (T).
- RNA base set: ${\text{A}, \text{C}, \text{G}, \text{U}}$ .
RNA typically exists as a single strand (one backbone) rather than a paired double helix.
Bases in RNA do not form the same canonical DNA base pairs in a fixed double-stranded arrangement as DNA does; the transcript notes that RNA is single-stranded and bases can be unpaired.
Comparison to DNA: RNA contains $2^{\prime}\text{-OH}$ on the ribose—distinct from DNA’s $2^{\prime}\text{-H}$ —and uses uracil in place of thymine.

ATP (adenosine triphosphate): a single nucleotide of ribose with adenine as its base and three phosphate groups.
- Formation: this triphosphate structure is what provides energy currency for cellular processes on a second-to-second basis.
- Summary: ATP = ribose + adenine + 3 phosphate groups.
Other nucleotides with energy/electron-transfer roles introduced: NAD+ and FAD+ (electron carriers).
- Roles: become important in cellular respiration, photosynthesis, and electron transfer processes.
- Relationship to nucleotides: these molecules are derived from nucleotides and participate in energy metabolism, separate from the information storage function of DNA/RNA.

There is a modeling activity for this section with three sets of materials.
Plan mentioned: work with three lab groups first; others can work on review questions, connect activities, or lab reports while waiting.
After the three groups finish, switch so the remaining students can participate.

DNA as information storage: the order of bases encodes genetic information used to direct protein synthesis.
Structure–function relationship: the backbone (covalent, stable) vs. base pairing (hydrogen bonds, reversible) enables both stability and accessibility for replication and transcription.
RNA’s role as a transient, single-stranded molecule with a different sugar and the presence of uracil reflect its specialized functions in transcription and translation.
Energy currencies and electron carriers (ATP, NAD+, FAD+) are essential for driving cellular processes and energy metabolism.
Practical implications: understanding DNA/RNA structure informs genetics, molecular biology techniques, biotechnology, and medicine.