How do cells convert the instructions of messenger RNA into proteins? What are the famous "gene machines" actually made of? And what happened when a World War II soldier suddenly ended up with a disease no one could cure?

In today's episode, we'll answer all these questions⎯and so many more⎯as we explore the last stage of the Central Dogma: translation.

Part 1: tRNA Structure

• The RNA Tie Club
• The Adaptor Hypothesis and Transfer RNA (tRNA)
• The Five Components of tRNA
• The 2D and 3D Structures of tRNA

Part 2: The Wobble Hypothesis

• Protein-Coding (Sense) vs. Non-Protein-Coding (Nonsense) Codons
• The Start Codon
• The Stop Codons
• Traditional Codon-Anticodon Pairing
• Wobble Pairing

Part 3: Amino Acid Activation (tRNA Loading)

• Reaction Coupling
• Formation of Aminoacyl-AMP
• Pyrophosphate Hydrolysis
• Formation of Aminoacyl-tRNA
• Aminoacyl-tRNA Synthetases

Part 4: The Ribosome

• Ribosomal RNA (rRNA)
• Understanding Svedberg Units
• The 70S and 80S Ribosomes
• The Role of the Nucleolus
• RNA Polymerases I, II, and III
• The A, P, and E Sites

Part 5: Prokaryotic Translation

• Polyribosomes
• Polycistronic mRNA
• The Shine-Dalgarno (SD) Sequence
• Initiation: Initiation Factors, Initiator tRNA, Formylmethionine, and the Translation Initiation Complex
• Elongation: Elongation Factors and the 3-Part Cycle
• Termination: Release Factors and Dissociation

Part 6: Eukaryotic Translation

• Monocistronic mRNA
• The 5' Cap Binding Site
• The Kozak Sequence
• Basics of Initiation, Elongation, and Termination
• Cap-Dependent Translation
• Internal Ribosome Entry Sites (IRES) and Cap-Independent Translation
• Post-Translational Modifications

References

• Clark, M. A., Douglas, M., & Choi, J. (2018). Biology 2e. OpenStax.
• Pallin, D. J., & Wright, J. (2022). MCAT: Biology review (3rd ed.). The Princeton Review.
• Urry, L. A., Cain, M. L., Wasserman, S. A., Minorsky, P. V., & Orr, R. B. (2021). Campbell: Biology (12th ed.). Pearson.

Further Reading

• Bilbray, B. P. (2012). Antibiotic treatments over the past century. Congressional Record.
• Crick, F. (1955). On degenerate templates and the adaptor hypothesis: A note for the RNA Tie Club. NIH.
• Crick, F. (1958). On protein synthesis. Wellcome Collection.
• Dole, B. (2005). One soldier's story. HarperCollins Publishers.
• Ramakrishnan, V. (2018). Gene machine: The race to decipher the secrets of the ribosome. Basic Books.

How is DNA converted into RNA?

In this episode, we continue our conversation in molecular biology by focusing on the first stage of the Central Dogma: transcription. We explore this process in tremendous detail⎯from the unique proteins involved in initiation, elongation, and termination to the many ways transcription differs between prokaryotes and eukaryotes.

Part 1: Overview

- Transcription

- RNA vs. DNA

- Prokaryotic and Eukaryotic RNA Polymerases

Part 2: Initiation

- The Prokaryotic Promoter: the -35 Sequence and the Pribnow Box

- The Eukaryotic Promoter: the TATA Box

- Open and Closed Complexes

- The Preinitiation Complex

- Transcription Factors

Part 2: Elongation

- The Transcription Bubble

- The Template and Non-Template Strand

Part 3: Termination

- Prokaryotic Termination: Rho-Dependent and Rho-Independent

- Eukaryotic Termination and the Polyadenylation Signal Sequence

- Processivity

Part 4: Eukaryotic Post-Transcriptional Modification

- Introns, Exons, and Splicing

- Alternative Splicing

- The 5' Cap

- The Poly(A)-Tail

What does DNA do, exactly? And how does it do it?

In this episode, we see how DNA's structure informs its role as a storage molecule for genetic information. We review the major experiments and discoveries that informed our present understanding of basic molecular biology. We also explore the many roles of proteins in the cell and how DNA utilizes a special genetic code to relay the instructions for protein synthesis.

Part 1: Discovering the Role of DNA

- The Functions of Proteins

- The Griffith Experiment and Bacterial Transformation

- The Avery-MacLeod-McCarty Experiment

- The Hershey-Chase Experiment

- Basics of the Genetic Code

Part 2: The Central Dogma

- The Role of Messenger RNA

- Overview of the Central Dogma

- Caveats to the Central Dogma

What is DNA? What is it made of? And how is it packaged in the cell?

In today’s episode, we’ll examine the molecular framework of DNA up close (like⎯extremely close) and explore how that structure expands to form the structure of an entire chromosome.

Part 1: Nucleotide Structure

- The Three Parts of a Nucleotide

- Riboses and Deoxyriboses

- Hallmarks of Aromatic Structure (including Hückel's Rule)

- Purines and Pyrimidines

- Phosphate Groups

- Phosphodiester Bonding and 5'-3' Orientation

Part 2: DNA Structure

- The History of the Watson-Crick Model

- Double-Stranded DNA

- Antiparallel Orientation

- Base-Pairing and Chargaff's Rules

- A-DNA, B-DNA, and Z-DNA

- Structural Dimensions of B-DNA

- Major vs. Minor Grooves

Part 3: Chromosome Structure

- Prokaryotes and Eukaryotes

- Supercoiling and DNA Gyrase

- Chromatin Structure

- Heterochromatin vs. Euchromatin

- Chromosome Formation and Condensin Proteins

- Centromere Positions

- Telomere Functions

How do biologists study life? What special building blocks make us "alive"? How do these building blocks work together⎯and what happens when things go wrong?

In our pilot episode, we’re starting off with a deep dive into biomolecules. We’ll talk about the structures and functions of proteins, carbohydrates, lipids, and nucleic acids. We’ll also review a couple of really important functional groups that show up again and again in the most significant biological molecules. And we'll get to the bottom of what biology is all about.