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GENETICS - CLUTCH

CH.10 TRANSCRIPTION

CONCEPT: OVERVIEW OF TRANSCRIPTION

● Transcription is the process of using DNA as a template to ___________________ RNA □ RNA polymerase is the enzyme that transcribes DNA

- There are many different types of RNA polymerases

□ RNA transcripts are _____________________ in the 5’ to 3’ direction by adding rNTPs onto the 3’ OH group

- Each gene is transcribed using only one strand of the double strand DNA

- Upstream means an area of DNA before the gene start site

- Downstream refers to an area after the gene start site

□ There are three stages of transcription: initiation, elongation, and termination

- These stages slight differ between prokaryotes and eukaryotes

EXAMPLE:

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PRACTICE:

1. Transcription is the process of which of the following? a. DNA à Protein b. DNA à RNA c. DNA à DNA d. RNA à DNA

2. True or False: Only one strand of DNA is used during transcription of a gene. a. True b. False

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3. If a DNA sequence is upstream of where the gene is, where is these sequence? a. Before the gene b. After the gene c. In the middle of an intron d. At the start of the first exon

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CONCEPT: PROKARYOTIC TRANSCRIPTION

● Prokaryotic transcription ______________________ from eukaryotic transcription □ Prokaryotic transcription initiation requires certain factors

- Promoters are sequences that signal for the start of transcription

- There are three prokaryotic promoter consensus sequences, meaning similar sequences

- Pribnow box (~10bp sequence) which is upstream of start site – 5’ TATAAT 3’

- 35 base pair consensus sequence

- -40 to -60 upstream sequence (occasionally there)

□ The RNA polymerase holoenzyme binds to the promoter

- Consists of a sigma factor and a core enzyme

- The sigma factor is a peptide sequence that controls specificity of the RNA polymerase

EXAMPLE:

□ Prokaryotic transcription elongation occurs __________________________ initiation

- Transcription bubble is a sequence of ~18 nucleotides of unwound DNA where transcription occurs

□ Prokaryotic transcription termination occurs when RNA polymerase reaches a specific ____________

- Termination sequences (terminators) are found upstream of the termination site

- Rho-dependent terminators cause termination in the presence of the rho protein

- Rho-independent terminators cause termination in the absence of the rho protein

- Intrinsic termination occurs in uracil rich RNA transcripts, as the bonds are weak

- Can cause disassociation of RNA polymerase and transcription termination

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□ Polycistronic mRNA is when a group of genes are transcribed into RNA in a ____________ strand

- A single terminator is present at the end of a group of genes

- These genes have to be processed into individual genes

EXAMPLE:

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PRACTICE:

1. Which of the following is not an example of a prokaryotic promoter sequence? a. TATA Box b. Pribnow Box c. 35bp consensus sequence d. -40-60 upstream consensus sequence

2. What is the purpose of a sigma factor in prokaryotic transcription? a. The sigma factor serves as a transcription initiator sequence b. The sigma factor controls the specificity of the polymerase c. The sigma factor forms the transcription bubble d. The sigma factor controls transcription termination

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3. True or False: Prokaryotic transcription can create polycistronic mRNA. a. True b. False

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CONCEPT: EUKARYOTIC TRANSCRIPTION

● Eukaryotic transcription is more _________________________ than prokaryotic transcription □ Diverse RNA polymerases transcribe different RNAs

RNA polymerase I Ribosomal RNA RNA polymerase II Messenger RNA RNA polymerase III tRNA

□ Transcription initiation requires many ______________________

- General transcription factors (GTFs) are proteins that are required to initiate transcription

- Ex: TFIIA, TFIIB, TFIID

- Promoter is a DNA sequence that initiation factors bind upstream of the gene transcript

- TATA-box is a sequence of Ts and As ~30 bp upstream of start site

- TFIID (TATA binding protein) binds this sequence and recruits GTFs

- GFTs bound to the promoter recruit RNA polymerase II

- Preinitation complex includes GFTs, RNA polymerase II at the promoter

EXAMPLE:

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□ Transcription elongation begins after transcription _____________________

- The carboxyl terminal domain on the RNA polymerase II controls elongation

- Phosphorylation of this tail occurs by GTFs

- When phosphorylated, it releases RNA polymerase II from the initiation complex

- Once released, RNA polymerase II elongates the transcript

□ Transcription termination doesn’t have to occur at a specific sequence

- RNA polymerase II transcribes 100s or 1000s of nucleotides past the coding sequence

- RNA processing forms the coding mRNA sequence

EXAMPLE:

□ A number of factors ____________________ transcription

- Enhancers activate and help enhance transcription

- Silencers repress transcription

- Specific transcription factors that work to activate or repress specific genes

□ These factors can be located near or far to the transcription start site

- Cis-acting elements are elements that are found within the same chromosome

- Trans-acting elements are elements that are found in other chromosomes

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EXAMPLE:

PRACTICE:

1. Which of the following polymerases is responsible for transcribing mRNA in eukaryotes? a. RNA polymerase I b. RNA polymerase II c. RNA polymerase III d. RNA polymerase

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2. Which of the following general transcription factors is responsible for binding to the TATA-Box a. TFIIA b. TFIIB c. TFIID d. TFIIH

3. Which of the following modifications occurs to the RNA polymerase tail in order to trigger it to elongate the transcript?

a. Methylation b. Acetylation c. Carboxylation d. Phosphorylation

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4. Which of the following regulatory mechanisms regulates transcription from a great distance away from the gene? a. Silencers b. Specific transcription factors c. Enhancers d. Promoters

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CONCEPT: mRNA MODIFICATION

● After transcription RNA goes through _________________ processing steps before translation □ It gets a 5’ cap through the attachment of a 7-methylguanosine molecule

- Protects RNA from degradation

- Important for translation

□ It gets a 3’ polyadenylation tail through adding 150-200 adenine nucleotides at the end

- A polyadenylation signal (AAUAAA) triggers the addition of the poly A tail

EXAMPLE:

● Splicing removes non-coding introns from the _______________ exons □ The Spliceosome splices the introns out of the pre-mRNA

- The spliceosome is made up of small nuclear RNAs (U1,U2,U4,U5,U6) and proteins

- We call the spliceosome small ribonucleoprotein complex (snRNP)

□ The spliceosome recognizes three sequences that are required for splicing

- The 5’ splice site is a GU

- The 3’ splice site a AG (called the GU-AG rule)

- Branch point is a single adenine nucleotide around 18-40 nucleotides upstream of the 3’ splice site

- The intron forms a lariat, which is a small circular structure, when it is excised from the pre-mRNA

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EXAMPLE:

● RNA editing is a form of post-transcriptional RNA ___________________ □ Substitution editing is when a nucleotide is changes

□ Insertional editing is when a nucleotide is added

□ Deletion editing is when a nucleotide is deleted

□ Guide RNAs are RNAs that choose where RNA editing will occur

EXAMPLE:

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PRACTICE:

1. Which of the following is NOT a method of mRNA modification? a. 5’ cap b. 3’ Poly-A tail c. Methylation d. Splicing

2. The spliceosome is made up of which of the following components? a. DNA and RNA b. RNA and Protein c. Only RNA d. Only Protein

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3. Which of the following is not a sequence that the spliceosome recognizes? a. 5’ GU b. 3’ AG c. Branch Point d. Splice Point

4. True or False: After transcription the RNA sequence cannot be changed or modified before translation. a. True b. False

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CONCEPT: RNA INTERFERENCE

● RNA Interference (RNAi) is a type of posttranscriptional regulation _______________________ through RNA □ miRNAs are a single stranded RNA that targets the degradation of many different RNA transcripts

- Initially, it is transcribed by RNA pol II as a part of a longer RNA

- Dicer is an enzyme that cleaves pre-miRNA into a ~22 nucleotide miRNA

- RISC complex binds the miRNA, which targets it to destroy a transcript

□ siRNAs are a double stranded RNA that targets the degradation of a specific transcript

- Initially, it is transcribed within the gene it regulates

- Dicer cleaves the pre-siRNA into the siRNA

- RISC unwinds and binds the ds-siRNA, which targets it to destroy a specific transcript

EXAMPLE:

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PRACTICE:

1. True or False: siRNAs target a variety of different RNA transcripts for degradation. a. True b. False

2. Which of the following enzymes are responsible for cleaving and processing miRNAs and siRNAs? a. DICER b. RISC c. Guide RNA enzymes d. RNA polymerase II

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3. MiRNAs and siRNAs target degradation of RNA transcripts by binding to what? a. RNA polymerase II b. The gene promoter c. A gene transcript d. The spliceosome

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