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PODCAST

Cellular and Molecular Biology for Research

Ahmadreza Gharaeian

Cellular and Molecular Biology for Research is the podcast where complex textbooks stop gathering dust and start making sense. Each episode breaks down the dense chapters of cellular and molecular biology—DNA, signaling pathways, protein folding, experimental techniques—into clear explanations for students, early-career researchers, or anyone who wants to actually understand the science instead of just memorizing it. Think of it as your study buddy who reads the heavy stuff, translates the jargon,

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All Episodes

01:02:04

DNA Replication, Damage, and Repair (CMB part 18)

Cellular and Molecular Biology for Research ·

2026/01/08

Several principles govern DNA replication across most organisms: (1) Double-stranded DNA replicates in a semiconservative manner, where the parental strands separate and serve as templates for the synthesis of new, complementary strands. (2) DNA replication in E. coli and other organisms is at least semidiscontinuous. One strand, often considered to replicate continuously in the direction of the replication fork's movement, may actually replicate discontinuously. The other strand replicates

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00:44:12

Ribosomes and Transfer RNA (CMB part 17)

Cellular and Molecular Biology for Research ·

2026/01/04

X-ray crystallography studies on bacterial ribosomes with and without tRNAs have revealed that tRNAs occupy the cleft between the two subunits. They interact with the 30S subunit through their anticodon ends and with the 50S subunit through their acceptor stems. The binding sites for tRNAs primarily consist of rRNA. The anticodons of tRNAs in the A and P sites come into close proximity, allowing base-pairing with adjacent codons in the mRNA bound to the 30S subunit, as the mRNA bends 45 degrees

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00:38:27

The Mechanism of Translation II (CMB part 16)

Cellular and Molecular Biology for Research ·

2025/12/28

Messenger RNAs are read in the 5' to 3' direction, which is the same direction in which are synthesized. Proteins are synthesized from the amino terminus to the carboxyl terminus, meaning the amino-terminal amino acid is added first. The genetic code consists of three-base sequences called codons in mRNA, which instruct the ribosome to incorporate specific amino acids into a polypeptide. The code nonoverlapping, meaning each base is part of only one codon, and it lacks gaps or commas, with every

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01:35:09

The Mechanism of Translation I: Initiation (CMB part 15)

Cellular and Molecular Biology for Research ·

2025/12/24

Two critical events precede protein synthesis. First, aminoacyl-tRNA synthetases attach amino acids to their respective tRNAs with high specificity through a two-step reaction that begins with the activation of the amino acid using AMP, derived from ATP. Second, ribosomes must dissociate into their subunits at the conclusion of each translation cycle. In bacteria, this dissociation is actively facilitated by RRF and EF-G, while IF3 binds to the free 30S subunit, preventing its reassociation with the

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00:59:56

Other RNA Processing Events and Post-Transcriptional...

Cellular and Molecular Biology for Research ·

2025/12/21

Ribosomal RNAs are synthesized in the nucleoli of eukaryotic cells as precursors that require processing to yield mature rRNAs. The sequence of RNAs in the precursor is universally 18S, 5.8S, and 28S across all eukaryotes, although the precise sizes of the mature rRNAs differ among species. In human cells, the precursor is 45S, which undergoes a processing scheme that produces 41S, 32S, and 20S intermediates, with snoRNAs playing crucial roles in these steps. Extra nucleotides are removed from the

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01:26:08

RNA Processing II: Capping and Polyadenylation (CMB...

Cellular and Molecular Biology for Research ·

2025/12/17

Capping occurs in several steps: initially, RNA triphosphatase removes the terminal phosphate from pre-mRNA. Subsequently, guanylyl transferase adds the capping GMP derived from GTP, followed by two methyl transferases that methylate the N7 position of the capping guanosine and the 2'-O-methyl group of the penultimate nucleotide. These processes take place early in transcription, before the RNA chain exceeds 30 nucleotides in length. The cap plays a crucial role in ensuring proper splicing of some

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00:55:25

RNA Processing I: Splicing (CMB part 12)

Cellular and Molecular Biology for Research ·

2025/12/14

Nuclear mRNA precursors undergo splicing through a lariat-shaped or branched intermediate. In addition to the consensus sequences at the 5′ and 3′ ends of nuclear introns, branchpoint consensus sequences are also present. In yeast, this sequence is almost invariant as UACUAAC, whereas in higher eukaryotes, the consensus sequence is more variable, represented as YNCURAC. In all cases, the branched nucleotide corresponds to the final A in the sequence. The yeast branchpoint sequence also determines

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01:22:11

Chromatin Structure and Its Effects on Transcription(...

Cellular and Molecular Biology for Research ·

2025/12/11

Eukaryotic DNA associates with basic protein molecules called histones to form nucleosomes. Each nucleosome consists of four pairs of histones (H2A, H2B, H3, and H4) arranged in a wedge-shaped disc, around which 146 base pairs (bp) of DNA are wrapped. Histone H1, which is not part of the core nucleosome, is more easily removed from chromatin than the core histones. In the second level of chromatin folding, both in vitro and presumably in vivo, a string of nucleosomes forms a 30-nanometer (nm) fiber

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01:37:51

Transcription Activators in Eukaryotes( CMB part 10)

Cellular and Molecular Biology for Research ·

2025/12/07

Eukaryotic activators consist of at least two domains: a DNA-binding domain and a transcription-activating domain. DNA-binding domains include motifs such as zinc modules, homeodomains, bZIP, or bHLH motifs. Transcription-activating domains can be acidic, glutamine-rich, or proline-rich. Zinc fingers are characterized by an antiparallel β-sheet followed by an α-helix. The β-sheet contains two cysteines, and the α-helix contains two histidines, which coordinate with a zinc ion to form the

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01:21:29

General Transcription Factors in Eukaryotes (CMB part 9)

Cellular and Molecular Biology for Research ·

2025/12/04

Transcription factors bind to class II promoters in vitro in the following sequence: (1) TFIID, with assistance from TFIIA, attaches to the TATA box. (2) TFIIB binds subsequently. (3) TFIIF facilitates the binding of RNA polymerase II. The remaining factors bind in this order:IIE and TFIIH, creating the DABPolFEH preinitiation complex. Notably, TFIIA's involvement appears to be optional in vitro.TFIID is composed of a TATA-box-binding protein (TBP) and 13 additional polypeptides referred to as

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00:56:31

Eukaryotic RNA Polymerases and Their Promoters (CMB...

Cellular and Molecular Biology for Research ·

2025/11/30

Eukaryotic nuclei house three distinct RNA polymerases, which can be separated using ion-exchange chromatography. RNA polymerase I resides in the nucleolus, while other two are located in the nucleoplasm. Each of these polymerases performs specific transcriptional roles. Polymerase I synthesizes a large precursor to the major rRNAs (5.8S, 18S, and 28S in vertebrates). Polymerase II generates hnRNAs, precursors to mRNAs, as well as miRNA precursors and most small nuclear RNAs (snRNAs). Polymerase III

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00:58:13

DNA–Protein Interactions in Bacteria(CMB part 7)

Cellular and Molecular Biology for Research ·

2025/11/26

The repressors of the λ-like phages possess recognition helices that fit sideways into the major groove of the operator DNA. Specific amino acids on the DNA-facing side of the recognition helix establish precise contacts with bases in the operator, and these interactions determine the specificity of the protein-DNA binding. Altering these amino acids can modify the specificity of the repressor. Both the λ repressor and the Cro protein exhibit affinity for the same operators, but their

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00:55:16

Major Shifts in Bacterial Transcription (CMB part 6)

Cellular and Molecular Biology for Research ·

2025/11/22

Bacteria undergo significant shifts in transcription patterns during various processes, such as phage infection or sporulation, and have evolved multiple mechanisms to facilitate these changes. For instance, the transcription of phage SPO1 genes in infected B. subtilis cells follows a temporal sequence, where early genes are transcribed first, followed by middle genes, and finally late genes. This transition is regulated by phage-encoded sigma factors that associate with the host's core RNA

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00:39:43

Operons: Fine Control of Bacterial Transcription (CMB...

Cellular and Molecular Biology for Research ·

2025/11/19

Lactose metabolism in E. coli is facilitated by two essential proteins, β-galactosidase and galactoside permease. The genes encoding these proteins, along with another enzyme, are organized into a cluster and transcribed together from a single promoter, producing a polycistronic mRNA. These functionally related genes are therefore regulated collectively. The lac operon is controlled through both positive and negative regulatory mechanisms. Negative regulation occurs as follows: the operon remains

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00:56:00

The Mechanism of Transcription in Bacteria (CMB part 4 )

Cellular and Molecular Biology for Research ·

2025/11/15

The catalytic agent in the transcription process is RNA polymerase. In E. coli, this enzyme consists of a core, which houses the fundamental transcription machinery, and a sigma factor (σ-factor), which guides the core to transcribe specific genes. The σ-factor facilitates the initiation of transcription by enabling the RNA polymerase holoenzyme to bind tightly to a promoter. This σ-dependent binding necessitates the localized melting of 10–17 base pairs of DNA near the transcription start site,

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01:03:21

Molecular Tools for Studying Genes and Gene Activity...

Cellular and Molecular Biology for Research ·

2025/11/09

Methods for purifying proteins and nucleic acids are fundamental in molecular biology. DNA, RNA, and proteins of varying sizes can be effectively separated using gel electrophoresis. Agarose is the most commonly used gel for nucleic acid electrophoresis, while polyacrylamide is typically employed for protein electrophoresis. Sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) separates polypeptides based on their sizes. For higher resolution, two-dimensional gel electrophoresis is

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01:14:47

Molecular Cloning Methods (CMB part 2)

Cellular and Molecular Biology for Research ·

2025/11/05

To clone a gene, it must be inserted into a vector capable of carrying the gene into a host cell and ensuring its replication. This insertion is typically achieved by cutting both the vector and the target DNA with the same restriction endonucleases to create matching “sticky ends.” Cloning vectors in bacteria are primarily categorized as plasmids or phages. Plasmid cloning vectors include pBR322 and the pUC plasmids. The pUC plasmids and pBS phagemids facilitate convenient screening, as they

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01:04:35

An intro to Molecular and Functional Properties of...

Cellular and Molecular Biology for Research ·

2025/11/01

The three primary functions of genes are storing information, replication, and the accumulation of mutations. Proteins, also known as polypeptides, are polymers of amino acids linked by peptide bonds. Most genes carry the instructions for producing a single polypeptide and are expressed through a two-step process: transcription, which synthesizes an mRNA copy of the gene, followed by translation, where this mRNA is used to produce a protein. Translation occurs on ribosomes, the cell’s protein

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01:09:44

Cancer and the Immune System ( Immunology final part )

Cellular and Molecular Biology for Research ·

2025/10/27

Cancer is characterized as a malignant tumor, defined by its ability to grow progressively, invade surrounding healthy tissues, and spread to distant sites through a process known as metastasis. These malignant cells are essentially altered versions of the body’s own cells, having escaped normal growth-regulating mechanisms and apoptotic signals, which leads to unchecked proliferation.From an immunological standpoint, the immune system plays a vital role in cancer surveillance as part of its regular

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01:25:02

Immunodeficiency Diseases( immunology part 18)

Cellular and Molecular Biology for Research ·

2025/10/23

Immunodeficiency diseases underscore the critical role of the immune system's cells and molecules in maintaining overall protection against disease. Primary immunodeficiency diseases, stemming from over 300 distinct inherited genetic defects, encompass a spectrum from severe SCID conditions affecting T cells and B cells to milder defects impacting the production of specific immunoglobulin classes or complement components. The most severe SCID cases obstruct the development of all hematopoietic

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