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PHS2102 > Lecture 11: transcription and its regulation > Flashcards

Lecture 11: transcription and its regulation Flashcards

1
Q

What are the names of the DNA strand that is used as a template to synthesize RNA?

A

template/non-coding/antisense/active strand

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2
Q

What is the process of transcription initiation in prokaryotes?

A
  1. The sigma factor binds to RNA polymerase
  2. It locates a promoter and binds to the TATA box
  3. Forms transcription initiation complex
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3
Q

What is the process of transcription elongation in prokaryotes?

A
  1. RNA polymerase unwinds DNA to form a transcription bubble
  2. After synthesizing 10 nucleotides, the sigma factor dissociates and RNA polymerase undergoes a series of conformational changes
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4
Q

What is the direction in which the growing RNA strand is synthesized?

A

5’ to 3’

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5
Q

What are the 2 types of translation elimination that can occur in prokaryotes?

A
  1. Rho independent
  2. Rho dependent
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6
Q

What are the 3 conserved features of the promoter?

A
  1. -35 region: TTGACA sequence located 35 nucleotides upstream
  2. -10 AT rich region located 10 nucleotides upstream, has the TATA box where the sigma factor binds
  3. +1 initiation site: first codon that gets transcribed
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7
Q

What is the process of Rho independent translation termination in prokaryotes?

A
  1. RNA polymerase transcribes the terminator sequence
  2. The RNA forms a hair pin structure
  3. This causes RNA polymerase to pause and dislodge from the DNA template
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8
Q

What is the process of Rho dependent translation termination in prokaryotes?

A
  1. The RNA transcript contains a binding site for the rho factor
  2. It slides along the RNA chain and chases after RNA polymerase
  3. Rho factor also has ATP dependent helicase activity so it is able to unwind the RNA from the DNA template as it moves
  4. It catches up to RNA polymerase and displaces it from the template
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9
Q

What is the process of transcription initiation in eukaryotes?

A
  1. TATA box binding protein binds to the TATA box sequence and unwinds DNA
  2. Transcription factors TFIIB and TFIIA bind
  3. RNA polymerase II recognises this complex and binds to it
  4. TFIIE, TFIIF and TFIIH bind to form the transcription initiation complex
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10
Q

How is transcription regulated?

A
  1. Activators: bind to enhancer sequences –> DNA looping mechanism –> activator interacts with regulatory proteins at the pre initiation complex –> maximize transcription
  2. Repressors: bind to silencers–> same mechanism
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11
Q

What is the process of transcription elongation in eukaryotes?

A
  1. TFIIH is also a helicase which unwinds the DNA helix
  2. It also phosphorylates RNA polymerase II which causes it to change its conformation and dissociate from the other proteins in the initiation complex
  3. RNA polymerase II moves along the DNA template and synthesizes RNA in the 5’ to 3’ direction.
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12
Q

What is the process of transcription termination in eukaryotes?

A
  1. Transcription can stop at varying distances downstream of the gene, there isn’t a specific termination site
  2. Transcript is cleaved at an internal site before RNA polymerase finishes transcription
  3. The remainder of the RNA after the cleavage site is digested by a 5’ exonuclease
  4. The exonuclease chases after RNA polymerase and disengages it from the template strand
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13
Q

What are the processes of post transcriptional processing of mRNA?

A
  1. 5’ end receives a methyl guanosine cap
  2. Poly-A-tail added to the 3’ end
  3. Removal of introns and splicing of exons
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14
Q

How many codons make up the entire genetic code?

A

64

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15
Q

What are the advantages of the degeneracy of the genetic code?

A
  1. It acts as a buffer against mutational disruption
  2. If a codon is misread, there’s a chance it still codes for the same amino acid
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16
Q

What is the name of the enzyme that couples a particular amino acid to its corresponding tRNA?

A

aminoacyl-tRNA synthetase

17
Q

Describe the process of translation initiation in eukaryotes.

A
  1. Recycling of post translational complexes to yield separated 40S and 60 ribosomal subunits
  2. Formation of the eIF2 + GTP and the Met-tRNA complex
  3. 40S subunit and other factors bind to this complex –> 43S complex
  4. mRNA activation where the mRNA cap-proximal region is unwound in an ATP dependent manner
  5. The mRNA attaches to the complex
  6. The complex scans the mRNA and binds to the initiation codon
  7. Dissociation of some factors and the binding of 60S subunit
  8. GTP hydrolysis and release of other factors
18
Q

Describe the process of translation initiation in prokaryotes.

A
  1. 3 initiation factors
  2. Initiation factors + met-tRNA + 30S subunit bind to Shine dalgarno sequence
19
Q

Describe the process of translation elongation.

A
  1. mRNA passes through the ribosomal subunits –> read in 5’ to 3’ direction
  2. tRNAs deliver amino acids to the ribosome in the order specified by mRNA
  3. peptide bond formation
20
Q

What is the name of the proteins that assist in the elongation process?

A

elongation factors

21
Q

What direction does the peptide chain grow in?

A

amino to carboxyl direction

22
Q

Describe the process of translation termination.

A
  1. Ribosome reaches stop codon
  2. Release factors bind to ribosome and promote the hydrolysis of the peptidyl-tRNA link to release the peptide chain from mRNA
23
Q

How do antibacterial agents like tetracycline inhibit translation?

A
  1. It binds specifically to the 30S ribosome of the bacteria
  2. Prevents the attachment of the aminoacyl tRNA to the RNA-ribosomal complex
  3. Blocks protein synthesis
24
Q

What are some of the possible post translational modifications that can occur in proteins?

A
  1. Folding of the polypeptide + covalent modifications
  2. Binding to cofactors
  3. Assembly with partner chain
25
Q

What are the types of glycosylation that occur?

A
  1. N linked
  2. O linked
  3. C linked
  4. Glypiation
  5. Phosphoglycosylation
26
Q

Which amino acid is involved in C linked glycosylation?

A

Tryptophan

27
Q

What is the function of glycosylation?

A
  1. In the ER, it ensures that only properly folded proteins are transported to the Golgi
  2. Facilitates their delivery to the correct destination
  3. Ligands to mediate cell attachment or stimulate signal transduction
  4. Oligosaccharides can be bulky which affects protein-protein interactions –> facilitate or inhibit
  5. Oligosaccharides are hydrophilic so they affect solubility

PHS2102 (15 decks)

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