Molecular Biology

What you'll learn

• Explain how the experiments of Griffith, Avery, MacLeod and McCarty, Hershey and Chase, and Chargaff identified DNA as the genetic material, describe the contributions of Franklin, Gosling, Wilkins, Watson and Crick to the double helix, and state the central dogma and its exceptions.
• Describe the structure of nucleotides, DNA and RNA, including antiparallel strands, base pairing, grooves and supercoiling; calculate reverse complements, GC content and melting temperatures; and explain how DNA is packaged into nucleosomes and chromatin.
• Explain semiconservative replication and the Meselson–Stahl experiment, and describe the roles of the origin, helicase, primase, DNA polymerases, sliding clamp, topoisomerases and ligase at a bacterial replication fork, including leading- and lagging-strand synthesis.
• Compare eukaryotic with bacterial replication, explain origin licensing, the end-replication problem and telomerase, relate telomere shortening to senescence and cancer, and calculate how base selection, proofreading and mismatch repair produce error rates of about one in a billion.
• Describe bacterial RNA polymerase and sigma factors, identify promoter elements and intrinsic terminators, distinguish template and coding strands, and model steady-state mRNA levels from synthesis and decay rates.
• Explain how RNA polymerase II and general transcription factors initiate transcription in eukaryotes, and describe capping, splicing (including alternative splicing and its role in diseases such as spinal muscular atrophy), polyadenylation, export and nonsense-mediated decay.
• Describe the genetic code and how it was deciphered, translate sequences and find open reading frames in six frames, and explain tRNA charging, wobble, and initiation, elongation and termination on bacterial and eukaryotic ribosomes, including antibiotic targets.
• Explain how proteins fold with the help of chaperones, how sorting signals direct them to cellular destinations, how proteolytic processing activates proteins such as insulin, and how post-translational modifications and the ubiquitin–proteasome system control protein function and lifetime.
• Explain negative and positive control of the lac operon, interpret partial diploids with the cis–trans test, model bistable induction, describe repression and attenuation of the trp operon, and outline riboswitches, small RNAs, quorum sensing and CRISPR immunity.
• Describe how chromatin modification, DNA methylation, transcription factors, enhancers and insulators, nuclear receptors, microRNAs and RNA-binding proteins regulate eukaryotic genes, and use binding equations to model transcription factor occupancy and cooperativity.
• Explain how restriction enzymes, gel electrophoresis, PCR, RT-qPCR and plasmid cloning work, predict digest fragments, design and check primers, estimate amplification and calculate relative expression by the ΔΔCt method.
• Explain Sanger and high-throughput sequencing, calculate sequencing coverage, normalize RNA-seq data, design CRISPR–Cas9 guide RNAs and interpret editing outcomes, explain how mRNA vaccines work, describe US oversight of recombinant DNA work under the NIH Guidelines, Institutional Biosafety Committees and the BMBL, and analyze an integrated investigation.