Molecular Biology: DNA, RNA, and Protein Synthesis

DNA Structure and Replication

DNA double helix (Watson & Crick, 1953): two antiparallel strands, complementary base pairing (A-T: 2 H-bonds, G-C: 3 H-bonds), 3.4 nm per turn, 10 base pairs per turn. B-form DNA predominant in cells; A-form in dsRNA; Z-form left-handed. Replication: semi-conservative (Meselson-Stahl experiment, 1958). Origin of replication → replication fork: helicase unwinds, SSB stabilizes, primase adds RNA primer. DNA polymerase III (prokaryotes): 5'→3' synthesis, 3'→5' proofreading exonuclease. Leading strand: continuous synthesis. Lagging strand: Okazaki fragments → RNA primers removed by RNase H → gaps filled by Pol I → ligase seals nicks. Error rate: ~10⁻¹⁰ per base pair per cell division (with mismatch repair).

Transcription

Transcription: DNA → mRNA, catalyzed by RNA polymerase. Prokaryotes: single RNA polymerase, σ factor recognizes promoter (-35, -10 TATA box). Eukaryotes: RNA Pol I (rRNA), Pol II (mRNA, snRNA), Pol III (tRNA, 5S rRNA). Promoter elements: TATA box, Inr, BRE — recognized by general transcription factors (TFIID/TBP, TFIIB, TFIIF, TFIIE, TFIIH). Elongation: RNA Pol II synthesizes pre-mRNA at ~40 nt/sec. Termination: poly(A) signal (AAUAAA) → cleavage and polyadenylation. Post-transcriptional processing: 5' capping (7-methylguanosine), 3' polyadenylation (200 A's), splicing (removal of introns by spliceosome — U1, U2, U4, U5, U6 snRNPs). Alternative splicing: one gene → multiple proteins (human: ~20,000 genes → ~100,000 proteins).

Translation and Protein Folding

Translation: mRNA → protein on ribosomes. Ribosome: 70S prokaryotic (30S + 50S), 80S eukaryotic (40S + 60S). tRNA: cloverleaf structure, anticodon pairs with mRNA codon, aminoacyl-tRNA synthetases charge with correct amino acid. Initiation: Shine-Dalgarno (prokaryotes) or 5' cap scanning (eukaryotes), start codon AUG = Met. Elongation: A-site (aminoacyl), P-site (peptidyl), E-site (exit); peptide bond formed by ribosomal RNA (ribozyme). Translation speed: ~15-20 amino acids/second in E. coli. Protein folding: primary → secondary (α-helix, β-sheet) → tertiary → quaternary. Chaperones (GroEL/GroES, Hsp70) assist folding. Misfolding → aggregation → disease (Alzheimer's amyloid-β, Parkinson's α-synuclein, prions).

Gene Regulation

Prokaryotic: operon model (Jacob & Monod, 1961). Lac operon: negative control (repressor), positive control (CAP-cAMP). Eukaryotic regulation: multi-level. Chromatin remodeling: histone acetylation (open chromatin, HATs) vs. deacetylation (closed, HDACs). Transcription factors: activators bind enhancers (up to 1 Mbp from promoter), repressors bind silencers. Mediator complex bridges TFs and RNA Pol II. Post-transcriptional: miRNA (RISC complex degrades mRNA), siRNA (RNA interference), RNA editing. Translational regulation: 5'UTR secondary structure, upstream ORFs, IRES elements. Post-translational: phosphorylation, ubiquitination (proteasomal degradation), SUMOylation.

Modern Techniques

PCR (Polymerase Chain Reaction, Mullis 1985, Nobel 1993): amplify specific DNA sequences. Real-time qPCR: quantitative measurement with fluorescent probes. Next-generation sequencing (NGS): Illumina (sequencing by synthesis), PacBio (SMRT, long reads), Oxford Nanopore (real-time, portable). Single-cell RNA-seq: transcriptome of individual cells — revealing cell type heterogeneity. CRISPR-Cas9 gene editing: guide RNA directs Cas9 nuclease to target site, DSB → NHEJ or HDR. Cryo-electron microscopy (cryo-EM): near-atomic resolution protein structures without crystallization (Nobel 2017). AlphaFold: AI-predicted protein structures for 200M+ proteins.

Try it live

Everything above runs in your browser — open DNA, RNA & Protein Synthesis and change the parameters while it is running. Nothing is installed, nothing is uploaded, the whole model lives in one tab.