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Z - Bio 2213 (Cell Biology) > Chapter 7 > Flashcards

Chapter 7 Flashcards

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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?

A

3

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
Q

What is wobble base pairing?

A

flexibility in 3rd base of codon, makes same amino acid

26
Q

What is the eukaryotic 80S ribosome made of? What is the name and role of its non-protein components?

A

Made of ribosomal proteins and rRNA, has a large and small subunit

rRNA - core of ribosome (gives structure), catalyze protein synthesis

27
Q

Describe the three sites of a eukaryotic 80S ribosome. Include the enzyme for peptide bond catalysis.

A

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
Q

Describe the process of translation relating to the ribosome sites starting from initiation (first tRNA) and ending with the final codon

A

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
Q

What is a proteosome?

A

Proteasome is a large protein machine that degrades proteins marked by ubiquitin

30
Q

Describe the chemical mechanism of initiation (binding to the mRNA)

Include all components and where the energy comes from

A

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
Q

Describe initiation in prokaryotes (attaching to RNA)

Include where binding occurs

A

Initiation factors bind to 30S ribosomal subunit

Initiator tRNA and mRNA bind to Ribosome Binding Site (RBS)

32
Q

Describe the transfer of energy for charging tRNAs, binding initiation factors, moving around amino acids,, and releasing

A

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
Q

What was the first codon whose amino acid pair was discovered?

A

A poly U sequence

34
Q

How were the matching amino acids for codons discovered?

A

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

Z - Bio 2213 (Cell Biology) (16 decks)

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