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Nucleic Acid Biochem III > 27 - The Ribosome > Flashcards

27 - The Ribosome Flashcards

616-624

1
Q

What type of structure is a ribosome?

A

ribonucleoprotein particle (RNP)

More contemporarily: ribozyme

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2
Q

What proportion of the ribosome is RNA? Protein?

A
  • 2/3 RNA

- 1/3 Protein

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3
Q

25% of the dried cell mass of an E.coli cells is?

A

Ribosomes, there are about 15,000 in a cell

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4
Q

What are the rRNAs that make a prokaryotic ribosome? (3)

A
  • 23S
  • 16S
  • 5S
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5
Q

What are the proteins that make a prokaryotic ribosome? (3)

A
  • L1
  • L2
  • L3
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6
Q

What are the subunits that make a prokaryotic ribosome? (2)

A
  • Large: 50S (5S+23S)

- Small: 30S (16S)

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7
Q

What is the sedimentation coefficient of a prokaryotic and eukaryotic ribosome?

A

Prokaryotic: 70S
Eukaryotic: 80S

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8
Q

All ribosomes contain two ________ (16S-18S, 23S-28S) and one or two small _____ (5S, 5.8S)

A

All ribosomes contain two major rRNA molecules (16S-18S, 23S-28S) and one or two small rRNAs (5S, 5.8S)

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9
Q

True or false? The SSU and LSU of ribosomes contain basically the same set of proteins.

A

False, the SSU and LSU contains different sets of proteins

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10
Q

What does an assembly map of the 30S ribosomal subunit show?

A

How a 30S ribosomal subunit of E. coli can be reassembled in the test tube from RNA and proteins, order of addition is important. Arrows indicate dependence in binding

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11
Q

What are the two structural features of the Small ribosomal subunit?

A
  • Head

- Base

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12
Q

What are the four structural features of the large ribosomal subunit?

A
  • Ridge
  • Valley
  • Central protuberance
  • Stalk
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13
Q

What three research methods were able to discern the secondary structure of 16S rRNA?

A
  • Chemical and enzymatic probing
  • Cross-linking studies
  • Comparative sequence analysis (phylogenetic approach)
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14
Q

Describe the secondary structure of E.coli’s 16S rRNA

A
  • Short range base pairing generating characteristic helices in various parts of the structure.
  • THere are long range base pairing regions that define four major folding domains (I-IV)
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15
Q

When homologous sequences (ie. sequences that share a common ancestor) are seen in the primary structure of ribosomal subunits, what does this indicate?

A

That these are anchor regions that align sequences

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16
Q

Comparative sequence analysis (phylogenetic approach) to discerning the secondary structure of ribosomal subunits looked for what two things?

A
  • Primary sequence identities (homologous anchors)

- Compensating base changes in putative helical regions of the secondary structure

17
Q

What is the universal core in ribosomes?

A

A region of the SSU and LSU (separate in the two units) that consists of non-contiguous (not immediately adjacent) segments of primary sequence that interact through complementary base pairing to form long range helices which divide the secondary structure into discrete folding domains (I, II, III and IV)

18
Q

What is evidence for the universal core being essential to the function of ribosomes?

A

It is highly conserved in both primary and secondary structures in different organisms and organelles.

19
Q

What are two points of evidence for RNA having a direct role in protein synthesis and what is the conclusion of them (concerning the universal core)?

A
  • LSU and SSU contains a highly conserved core of primary and secondary structure (universal core)
  • When mRNA and tRNA interact, specific nucleotides in functionally important regions of these RNAs can be chemically cross linked to selected universal core nucleotides in SSU and LSU rRNAs

This means that these critical mRNAs and tRNA nucleotides are positions within and probably interact with the universal core region of rRNA

20
Q

In addition to evidence about the universal core of rRNA having a direct role in protein synthesis, what is further evidence that ribosomal RNA has a direct role in protein synthesis before x-ray crystallography? (3)

A
  • Some antibiotics that inhibit protein synthesis bind to specific core nucleotides
  • Mutations in universal core nucleotides make ribosomes resistant to antibiotics that normally bind to these nucleotides
  • Large ribosomal subunits that have been stripped of protein are still able to carry out peptide bond synthesis (although complete deproteinization destroys this activity)
21
Q

What evidence was the final proof needed for RNAs functional importance in ribosomes?

A

x-ray crystallography proved that the active site is within the universal core and entirely surrounded by rRNA, not proteins.

22
Q

What are the tRNA binding sites on the ribosome? What subunit are they in?

A

E (empty)
P (peptidyl)
A (aminoacyl)

In the large subunit (LSU)

23
Q

What came first for the ribosome, RNA or protein?

A

Original ribosome consisted only on rRNA, ribosomal proteins came later

24
Q

What is the function of proteins in ribosomes?

A

To provide scaffold support and to stabilize the tertiary structure of rRNA in its catalytically active conformation

25
Q

How does the ribosome accelerate peptide-bond formation? (3)

A
  • Positioning substrates
  • Reorganizing water in the active site
  • Providing electrostatic network that stabilizes reaction intermediates
26
Q

Describe proton transfer during peptide bond formation

A

Proton transfer during the reaction seems to be promoted by a concerted shuttle mechanism that involves ribose hydroxyl groups on the tRNA substrate

27
Q

How is rRNA produced?

A

rDNA units tandemly linked together (one after another) and transcribed in the nucleolus. Along an rDNA repeat unit a ‘christmas tree’ looking structure appears. Each primary transcript comes out of a processome.

28
Q

What are the components of a primary ribosomal (rRNA) transcript? How is it modified?

A
  • Mature rRNA
  • Spacers
  • The RNA is modified with 2’-O-methyls and pseudouridines
  • Spacer sequences are removed by the action of exo and endoribonucleases
  • Mature rRNAs are folded and assembled with ribosomal proteins

All modifications happen at the same time

29
Q

What are the two types of spacers in ribosomal (rRNA) primary transcript?

A

External transcribed spacer (ETS)

Internal transcribed spacer (ITS)

30
Q

How are ribosomes made in eukaryotes (ribosome biogenesis)? Starting with the ribosomal (rRNA) primary transcript

A
  1. The 45S rRNA transcript is packaged into a large ribonucleoprotein particle (RNP) in the nucleolus, containing many ribosomal proteins imported from cytoplasm.
  2. Sites in the rRNA are modified and spacer sequences in the rRNA are discarded
  3. Large and small ribosomal subunits are exported from the nucleus individually
31
Q

What type of rRNA modifications take place in eubacteria?

A

Only a few sites of pseudouridine and 2-O’-methylation (Nm) occur

Unique proteins catalyze modifications at each of these sites

32
Q

What type of rRNA modifications take place in eukaryotes and archaea?

A

many more sites of rRNA modifications occur in eukaryotic and archaeal rRNA than in eubacteria

33
Q

What is the significance to rRNA modifications?

A

Modified residues are positioned close to the ribosome active site, the peptidyl transferase centre (PTC), suggesting they contribute to structure/function

Nucleic Acid Biochem III (10 decks)

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