Chapter 7 Flashcards

1
Q

What is the general purpose of mRNA?

A

Codes for protein

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2
Q

Where and when is mRNA processed? Why can it work that way (location of modifying factors)?

A

In the nucleus during transcription

modifying factors are docked on the phosphorylated C-terminus tail of RNAPII

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3
Q

What is the relationship between the nucleolus and RNA?

A

It is the site of most rRNA synthesis and ribosome subunit assembly

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4
Q

Where and how does mRNA leave its processing site? What factors are required and what changes does it undergo?

A

Require 5* cap, exon junctions, and polyA tail

Passes through nuclear pore complex

Once in cytoplasm, 5* cap is exchanged for an initiation factor for protein synthesis

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5
Q

What is RNA capping and what is its purpose?

A

Helps with export from the nucleus, stability, and translation

Made up of a modified guanosine nucleotide on the 5* end of the RNA
Attached by 5→5 triphosphate bridge

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6
Q

What is polyadenylation and what is its purpose? How is it created?

A

Helps with export from the nucleus, stability, and translation

AAUAAA sequence signals for downstream cleavage by nuclease

Poly(A) polymerase adds AMP to the chain (ATP → PP + AMP)

Length of tail correlates with stability

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7
Q

Do prokaryotes, eukaryotes, or both have introns?

A

Only eukaryotes

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8
Q

What does an exon junction complex do?

A

Recognizes two exons spliced together

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9
Q

What are the conserved sequences for introns and exons? (general)

A

conserved sequences that mark the boundary and an A within the intron that serves as a branch point

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10
Q

Do introns have a purpose?

A

Yes, encode some small RNAs and are involved in cell differentation

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11
Q

Describe the chemical mechanism for the removal of introns (ignore enzymes for now)

A

Two transesterification reactions result in cleavage first at the 5* end then the 3* end of the intron, followed rapidly by ligation of the two exons

Intermediate formation of a lasso (lariat) with “A” as branch point

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12
Q

What does the spliceosome do? What is it made of (describe)? What do U1 and U2 do?

A

Catalyzes cleavage of intron and ligation of exon

Make of 5 snRNPs (Several proteins and a snRNA)

snRNA base pair with splitting sites and branch points

U1 recognizes splice site, U2 recognizes branch point

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13
Q

What is the purpose of alternative splicing?

A

Different mRNA/protein from same gene

Cell differentiation

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14
Q

Describe RNA world

A

RNA can act as template and catalyst (ribozyme) and is easier to synthesize than DNA, may have been first

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15
Q

What binds to the promoter in prokaryotes? Are there any conserved sequences?

A

Sigma factor, 2 (don’t need to know location, help sigma factor find promoter)

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16
Q

How many RNA polymerases do eukaryotes have?

17
Q

What is the TATA box?

A

Conserved sequence upstream of the start of transcription

18
Q

What is transcription factor IID?

A

The transcription factor that is the first to find DNA, its TBP protein recognizes the TATA box and bends the DNA

19
Q

What is transcription factor IIH?

A

Acts as a helicase (uses ATP hydrolysis) and covalently adds phosphates to the tail of RNA polymerase II, a type of kinase

20
Q

Describe eukaryotic initiation

A

The polymerase and its transcription factors all bind to the DNA and start transcribing when TFIIH opens the DNA helix and phosphorylates the tail of RNA Polymerase II

21
Q

What are tRNAs? (general)

A

adaptors between mRNA and amino acid during protein synthesis

22
Q

What adds amino acids to tRNA? How? What is a ‘charged’ tRNA called?

A

Amino acyl tRNAsynthestases add amino acids to tRNA via ATP→AMP, 20 types

Charged tRNA is called an amnoacyltRNA

23
Q

Where does the energy for peptide bond formation come from?

A

Forming the bond between the amino acid and tRNA takes energy (ATP→AMP)

Breaking releases energy, catalyzes peptide bond formation

24
Q

How do anticodons work? Give an example (ex: if the anticodon is 5* GCC 3*

A

Anti-codons base pair with codons and go 3→5 rather than 5→3
Ex: anticodon 5GCC3 pairs with 3CGG5 which is really 5GGC3 or Gly

25
What is wobble base pairing?
flexibility in 3rd base of codon, makes same amino acid
26
What is the eukaryotic 80S ribosome made of? What is the name and role of its non-protein components?
Made of ribosomal proteins and rRNA, has a large and small subunit rRNA - core of ribosome (gives structure), catalyze protein synthesis
27
Describe the three sites of a eukaryotic 80S ribosome. Include the enzyme for peptide bond catalysis.
A Site: Where all aminoacyl tRNAs (except initiator tRNA) enter the ribosome P Site: Peptidyl site, where the peptide bond is formed Catalyzed by peptidyl transferase, a ribozyme (catalytic RNA) E Site: Exit site, where tRNAs leave ribosome
28
Describe the process of translation relating to the ribosome sites starting from initiation (first tRNA) and ending with the final codon
Initiator tRNA carrying anticodon for AUG binds to P site, then second tRNA binds to A site and its amino acid is peptide bonded to the start codon. tRNA in P site moves to E and A moves to P. Synthesis continues until release factor binds to A site. Release factor is a protein that resembles a tRNA and hydrolyzes GTP to release amino acid.
29
What is a proteosome?
Proteasome is a large protein machine that degrades proteins marked by ubiquitin
30
Describe the chemical mechanism of initiation (binding to the mRNA) Include all components and where the energy comes from
When the initiator tRNA and the small ribosomal subunit bind to the mRNA Many initiation factors (eIFs) also bind to sununit and mRNA. They recognize 5* cap and subunit/tRNA moves to find AUG Then GTP is hydrolyzed by eIF2s, the eIFs release, and large subunit joins complex
31
Describe initiation in prokaryotes (attaching to RNA) Include where binding occurs
Initiation factors bind to 30S ribosomal subunit Initiator tRNA and mRNA bind to Ribosome Binding Site (RBS)
32
Describe the transfer of energy for charging tRNAs, binding initiation factors, moving around amino acids,, and releasing
ATP → AMP for each charged tRNA Hydrolyze GTP → Initiation factors 2 GTP per amino acid → guide to A site, translocation Hydrolyze GTP → Release site
33
What was the first codon whose amino acid pair was discovered?
A poly U sequence
34
How were the matching amino acids for codons discovered?
Started with a poly U sequence, then made AAA and CCC Then could create any RNA sequence, but could not control reading frame Then made three nucleotide codons Captured a complex of ribosome, mRNA codon, and aminoacyl-tRNA