Biotech Institute

Fundamentals

What is Biotechnology?

Biotechnology applies biological systems and living organisms to develop technologies and products. Modern biotech spans genomics, protein engineering, gene editing, synthetic biology, and bioinformatics — using computational tools to understand and manipulate the molecular machinery of life.

Key Concepts

• DNA & RNA — DNA stores genetic information as a double helix of nucleotide bases (A, T, G, C). RNA (using U instead of T) transcribes and translates that code into proteins.
• Protein Structure — primary (sequence), secondary (alpha helices, beta sheets), tertiary (3D fold), quaternary (multi-subunit complexes). Structure determines function.
• CRISPR-Cas9 — programmable gene editing. A guide RNA directs the Cas9 nuclease to a specific DNA sequence, where it cuts. The cell's repair machinery introduces changes.
• PCR — Polymerase Chain Reaction amplifies specific DNA segments exponentially. Denature, anneal primers, extend with polymerase. Foundation of molecular biology.
• Sequencing — reading the order of nucleotides in DNA/RNA. Sanger (first-gen), Illumina (short-read NGS), Nanopore/PacBio (long-read).
• Phylogenetics — reconstructing evolutionary relationships from sequence data. Multiple sequence alignment, tree building (ML, Bayesian), molecular clocks.

Central Dogma

• DNA is transcribed into mRNA by RNA polymerase.
• mRNA is translated into protein by ribosomes, reading codons (3-nucleotide sequences) and assembling amino acids.
• Proteins fold into 3D structures that carry out virtually all cellular functions — enzymes, receptors, structural components.
• Epigenetics, RNA interference, and post-translational modifications add layers of regulation beyond the simple DNA-to-protein flow.

Free Courses

Textbooks

• Alberts et al: Molecular Biology of the Cell — THE cell biology textbook. Free online via NCBI Bookshelf. Covers everything from DNA replication to cell signaling.
• Lodish et al: Molecular Cell Biology — Comprehensive and accessible. Strong on gene expression, protein targeting, and signaling pathways.
• Lesk: Introduction to Bioinformatics — Covers databases, sequence alignment, phylogenetics, protein structure prediction, and genomics.
• LibreTexts: Genetics — Free, open-access genetics textbooks. Mendelian genetics, molecular genetics, population genetics.
• Nature Scitable — Free peer-reviewed science library. Topic pages on genetics, gene expression, cell biology, and evolution.

Key Research Papers

Open-Source Tools

Hardware & Providers

Reference

Molecular Biology

• DNA Replication — semiconservative; helicase unwinds, primase lays RNA primers, DNA polymerase III synthesizes, ligase seals Okazaki fragments
• Transcription — RNA polymerase reads DNA template 3'→5', synthesizes mRNA 5'→3'. Promoter recognition, elongation, termination.
• Translation — ribosome reads mRNA codons, tRNA delivers amino acids. Initiation (AUG), elongation, termination (UAA/UAG/UGA).
• Gene Regulation — operons (prokaryotes), transcription factors, enhancers, epigenetics (methylation, histone modification), miRNA.

Techniques

• PCR — 3-step thermal cycling: denature (95C), anneal primers (55-65C), extend (72C). Exponential amplification: 2^n copies after n cycles.
• CRISPR — design sgRNA complementary to target, Cas9 makes double-strand break, NHEJ (knockout) or HDR (knock-in) repairs the cut.
• NGS — library prep (fragment + ligate adapters), cluster generation, sequencing by synthesis, base calling, alignment, variant calling.
• Gel Electrophoresis — separate DNA/RNA/protein by size in an electric field. Agarose (DNA) or polyacrylamide (protein/SDS-PAGE).

Bioinformatics

• Sequence Alignment — Needleman-Wunsch (global), Smith-Waterman (local), BLAST (heuristic). Substitution matrices (BLOSUM, PAM).
• Phylogenetics — distance (neighbor-joining), parsimony, maximum likelihood (RAxML), Bayesian (MrBayes, BEAST).
• Genome Assembly — de Bruijn graphs (short reads), overlap-layout-consensus (long reads). SPAdes, Hifiasm, Flye.
• Structure Prediction — homology modeling, ab initio (Rosetta), deep learning (AlphaFold2, ESMFold). CASP competition benchmark.

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