DNA and RNA

DNA

is the universal storage molecule for genetic information. Board questions often focus on its structural directionality and stabilizing forces.

Double Helix

Two polynucleotide chains wound around a common axis in a right-handed spiral (B-DNA is the most common physiological form)

Antiparallel Orientation

The two strands run in opposite directions. One strand runs 5' → 3', while the complementary strand runs 3' → 5'

The Backbone

Formed by alternating 2'-deoxyribose sugars and phosphate groups linked by 3',5'-phosphodiester bonds. This backbone is highly negatively charged due to the phosphate groups.

Base Pairing (Chargaff’s Rules)

The rungs of the ladder are hydrophobic nitrogenous bases held together by hydrogen bonds.

• Adenine (A) = Thymine (T): 2 hydrogen bonds.

• Guanine (G) ≡ Cytosine (C): 3 hydrogen bonds. (Higher G-C content increases the melting temperature of the DNA).

Major and Minor Grooves

The asymmetric twisting of the helix creates grooves where proteins (like transcription factors) and drugs can bind.

RNA

is typically single-stranded, uses ribose (which has a reactive 2'-OH group, making RNA more prone to degradation), and substitutes Uracil for Thymine.

Ribosomal RNA (rRNA)

Abundance: ~ 80% (Most abundant)

Structural Features: Associates with proteins to form the large and small ribosomal subunits.

Primary Function: Structural and catalytic component of ribosomes (acts as a ribozyme to form peptide bonds).

Transfer RNA (tRNA)

Abundance: ~ 15%

Structural Features: Cloverleaf secondary structure; contains an anticodon loop and an amino acid attachment site at the 3’ end (CCA sequence).

Primary Function: Carries specific amino acids to the ribosome during translation.

Messenger RNA (mRNA)

Abundance: ~ 5% (least abundant)

Structural Features: Linear strand synthesized from a DNA template; read in triplets called codons

Primary Function: Carries the genetic code from the nucleus to the cytoplasm for protein synthesis.

Replication (DNA → DNA)

• Process: The duplication of the entire genome prior to cell division. It is semi-conservative (each new double helix has one old strand and one new strand).

• Key Enzyme: DNA Polymerase (synthesizes the new strand strictly in the 5' → 3’ direction).

Transcription (DNA → RNA)

• Process: The synthesis of an mRNA molecule from a specific DNA gene template.

• Key Enzyme: RNA Polymerase.

• Post-Transcriptional Modifications: Eukaryotic mRNA must be processed before leaving the nucleus (addition of a 5’ Cap, a 3’ Poly-A tail, and the splicing out of non-coding introns).

Translation (RNA → Protein)

• Process: The ribosome reads the mRNA codons, matches them with the correct tRNA anticodons, and synthesizes a polypeptide chain.

• Location: Cytoplasm or Rough Endoplasmic Reticulum.

microRNAs (miRNAs)

These are small, non-coding RNA molecules (typically about 22 nucleotides long) that act as master regulators of gene expression. When they bind to a complementary sequence on a target messenger RNA (mRNA), they recruit a protein complex (RISC) that either physically blocks the ribosome from translating the mRNA or cleaves the mRNA so it is destroyed. This is known as RNA interference or gene silencing.

Translating mRNA to peptides

This is the coordinated function of rRNA (acting as the catalytic ribosome) and tRNA (delivering the amino acids)

Splicing introns

This is performed by snRNAs (small nuclear RNAs), which combine with proteins to form the spliceosome complex in the nucleus

Carrying formylated methionine

This is the specific job of the initiator tRNA in prokaryotic bacteria (tRNAf^Met) to start the translation process

Synthesizing primers

This is the function of the enzyme Primase (a specialized RNA polymerase), which lays down short RNA primers so DNA Polymerase can begin DNA replication.