Notes

lecture 8 9
# *Slide 1: Introduction to Transcription*
- *Explanation: This slide introduces transcription. Transcription is when the cell makes a copy of a gene from DNA into a molecule called **RNA*. The copy helps the cell know how to make proteins.

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### *Slide 2: RNA (Ribonucleic Acid)*
- *Picture: A diagram of the **RNA* molecule showing a *single strand* with a backbone of sugar and phosphate, and bases (A, U, C, G).
- *Explanation: **RNA* is like a messenger that carries instructions from the DNA in the nucleus to other parts of the cell. It looks like a twisted ladder but it’s a single strand, unlike DNA, which is double-stranded.

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### *Slide 3-4: Transcription*
- *Picture: A picture showing the **DNA* and how *RNA polymerase* moves along the DNA, copying it into RNA.
- *Explanation: This diagram shows **RNA polymerase, an enzyme, moving along the DNA. It’s like a robot that reads the DNA and makes a copy of it into **RNA*, which is then used to make proteins.

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### *Slide 5-6: RNA Synthesis = Transcription*
- *Picture: A diagram showing **RNA polymerase* adding RNA bases to the DNA template.
- *Explanation*: This picture shows how RNA polymerase adds the correct RNA bases to make the RNA strand match the DNA template. It's like filling in the blanks in a workbook, where the DNA is the answer sheet.

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### *Slide 7: Transcription Mechanism*
- *Picture: A diagram showing how **RNA polymerase* and *transcription factors* help in making RNA from DNA.
- *Explanation: The **RNA polymerase* and helper proteins (called *transcription factors*) work together to start transcription. It's like having a team that works together to open a book and copy the text into a notebook.

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### *Slide 8-9: Basic Mechanism of Transcription*
- *Picture: A picture of **RNA polymerase* matching RNA bases with the DNA template.
- *Explanation: The enzyme **RNA polymerase* reads the DNA and creates a matching RNA strand. The DNA is like a guidebook, and RNA polymerase is like a reader copying the information word by word.
we need to know how the transcription work

1) Substrates: You need the right ingredients to copy the recipe. In transcription, the "ingredients" are special molecules called nucleoside triphosphates. These are like the building blocks needed to create the new RNA.

2)Base pairing rule: When you copy the recipe, you follow a rule about matching letters. In DNA, the letters are A, T, C, and G. A (adenine) always pairs with T (thymine), and C (cytosine) always pairs with G (guanine). In RNA, though, A pairs with U (uracil) instead of T. This is the "base pairing rule."

3) Catalyzes the formation of phosphodiester bonds: This is just a fancy way of saying that the copying process helps to link the ingredients (nucleotides) together. The copying machine makes sure they are joined correctly, forming a long chain (like a necklace) that is the RNA.

4) Elongation of the thread: As the copying happens, the new RNA strand gets longer and longer. This is called "elongation," and it means the RNA is being built piece by piece.

5) Template molecule is double-stranded DNA: The DNA is like the original cookbook. But to make a copy, part of the DNA "unzips" so one side can be read to make the RNA. This is like opening the cookbook to just one page so you can copy a recipe

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### *Slide 10: Differences from DNA Replication*
- *Picture: A comparison of **DNA replication* and *RNA transcription*.
- *Explanation: This shows how **transcription* is different from *DNA replication*. Unlike DNA replication, transcription doesn’t need a primer, and it only makes a single strand of RNA instead of two strands of DNA.

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### *Slide 11: RNA Polymerase and Template DNA*
- *Picture: A diagram showing **RNA polymerase* moving along the DNA and creating RNA.
- *Explanation: This diagram shows how **RNA polymerase* reads the DNA and creates an RNA strand. The RNA polymerase is like a typewriter that types out a message based on what it reads from the DNA.

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### *Slide 12: Gene Regulation*
- *Picture*: A diagram showing how different genes are transcribed in different cells.
- *Explanation*: This shows how different cells in the body (like muscle cells and brain cells) use different genes, even though they have the same DNA. It's like having a recipe book with many recipes, but each person picks different ones to cook.

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### *Slide 13: Transcription Unit*
- *Picture: A diagram of a **transcription unit* with a *promoter, **coding sequence, and **terminator*.
- *Explanation: A transcription unit is the section of DNA that gets copied into RNA. The **promoter* is like a “start here” sign, the *coding sequence* is the instructions for the protein, and the *terminator* is like a “stop here” sign.

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### *Slide 14: Starting Transcription*
- *Picture: A diagram showing how transcription starts at the *+1** site.
- *Explanation: Transcription begins at a specific spot on the DNA called *+1**. It’s like starting a race at the starting line.

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### *Slide 15: Prokaryotic vs. Eukaryotic Transcription*
- *Picture: A comparison between **prokaryotes* (like bacteria) and *eukaryotes* (like humans) in how they organize their genes.
- *Explanation: In **prokaryotes, many genes can be transcribed together in one go (like many recipes in one book). In **eukaryotes*, each gene is usually transcribed separately (like each recipe in its own book).

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### *Slide 16-17: Steps in Transcription*
- *Picture: A flow chart showing the three main steps of transcription: **initiation, **elongation, and **termination*.
- *Explanation*: Transcription has three steps:
1. *Initiation*: RNA polymerase starts transcription.
2. *Elongation*: RNA polymerase makes the RNA chain.
3. *Termination*: The RNA chain is completed and released.

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### *Slide 18: Operons in Prokaryotes*
- *Picture: A diagram showing **operons* in prokaryotes, where genes for related jobs are grouped together.
- *Explanation: In **bacteria, genes that help the bacteria do similar jobs are grouped together in a single "unit" called an **operon*. It’s like putting all the ingredients for a recipe in one basket.

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### *Slide 19-22: RNA Polymerase in Prokaryotes*
- *Picture: A diagram showing the structure of **RNA polymerase* in bacteria with subunits like *α, **β, and **σ*.
- *Explanation: RNA polymerase in bacteria is made of parts called **subunits*. Each part has a special job, like putting together the pieces of a puzzle to create the RNA.

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### *Slide 23-25: Promoters in Prokaryotes*
- *Picture: A diagram showing the *-10** and *-35* regions of a *promoter* that help RNA polymerase start transcription.
- *Explanation: The **promoter* is where RNA polymerase starts. The *-10* and *-35* regions are like special markers that tell RNA polymerase where to begin.

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### *Slide 26: Consensus Sequences*
- *Picture: A diagram showing the **TATAAT* and *TTGACA* sequences in the promoter.
- *Explanation: The **TATAAT* and *TTGACA* sequences are the most common starting points for RNA polymerase to begin making RNA. They help RNA polymerase find the right place to start working.

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### *Slide 27-29: Strength of Promoters*
- *Picture: A chart showing how **stronger* promoters make more RNA.
- *Explanation*: Stronger promoters, which match the ideal sequence better, help RNA polymerase make more RNA. It’s like having a better starting signal for a race.

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### *Slide 30-32: Inducible Genes and the Lac Operon*
- *Picture: A diagram of the **lac operon* in E. coli showing how lactose controls gene expression.
- *Explanation: The **lac operon* in bacteria is a group of genes that help digest lactose. These genes are *inducible*, meaning they are turned on when lactose is present.

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### *Slide 33-36: Transcription Initiation and Elongation*
- *Picture: Diagrams showing the process of **RNA polymerase* moving along the DNA and making RNA.
- *Explanation: **Initiation* is when RNA polymerase starts working, *elongation* is when it makes the RNA, and *termination* is when it finishes and releases the RNA.

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### *Slide 37-40: Polymerase Escaping the Promoter*
- *Picture*: A diagram showing how RNA polymerase "escapes" the promoter after making a short RNA.
- *Explanation*: RNA polymerase starts making RNA at the promoter but has to "escape" and start making a full RNA chain.

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### *Slide 41-43: Proofreading and Elongation*
- *Picture: A diagram showing how **RNA polymerase* corrects mistakes by proofreading.
- *Explanation: RNA polymerase can make mistakes, but it has two ways to fix them: **pyrophosphorolytic editing* and *hydrolytic editing*. These help it make the RNA as accurate as possible.

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### *Slide 44-45: Termination in Prokaryotes*
- *Picture: Diagrams showing **rho-dependent* and *rho-independent* termination in prokaryotes.
- *Explanation*: There are two ways transcription ends in bacteria:
- *Rho-dependent: The **rho* protein helps stop transcription.
- *Rho-independent: The RNA folds into a **hairpin loop*, which causes RNA polymerase to stop.

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### *Slide 46: Transcription in Mitochondria and Chloroplasts*
- *Explanation*: Mitochondria and chloroplasts have their own special RNA polymerases, similar to the ones in bacteria.

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### *Slide 47-49: Transcription in Eukaryotes*
- *Explanation*: In eukaryotes, there are three different RNA polymerases (I, II, and III) for making different types of RNA.

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### *Slide 50-51: RNA Polymerase Sensitivity*
- *Explanation*: Different RNA polymerases are sensitive to different chemicals. This helps control how they work.

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I’ll stop here for now, but let me know if you'd like me to continue explaining the remaining slides or if you'd like any part of this explanation clarified further!