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MCB 2 > I. DNA & RNA| 12. Characterization, role and synthesis of different types of RNA > Flashcards

I. DNA & RNA| 12. Characterization, role and synthesis of different types of RNA Flashcards

1
Q

What are the general structure and function of RNA?

A
  • RNA (Ribonucleic acid) = ribose sugar + nitrogenous base (A, C, G, U) + phosphate, function in many roles, such as: coding, decoding, regulation and expression of genes.
  • Often in nature as a single-strand folded onto itself (ex: tRNA), rather than a paired double strand
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2
Q

I. Types of RNA and biological importance
1. What are 2 types of protein-coding RNA?

A
  • mRNA (messenger RNA)
  • pre-mRNA
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3
Q

I. Types of RNA and biological importance - Protein-coding RNA
2. What are the features of mRNA (messenger RNA)?

A
  • carries information from DNA to the ribosome, the site of protein synthesis
  • the coding sequence in mRNA determines the amino acid sequence in the protein that is produced
  • only 3-5% of all RNA, because majority of RNA does not code for proteins
  • processed + matured with 5’-cap and poly-A tail
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4
Q

I. Types of RNA and biological importance - Protein-coding RNA
2. What are the features of pre-mRNA?

A
  1. precursor of mRNA = not processed mRNA yet
  2. with introns, but without 5’-cap and poly-A tail
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5
Q

I. Types of RNA and biological importance - Protein-coding RNA
3. What does hnRNA (heterogenous nuclear RNA) include?

A

hnRNA (heterogenous nuclear RNA) includes the pre-mRNA and the RNA- processing intermediates which contain 1 or more introns

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6
Q

I. Types of RNA and biological importance - Non-coding RNA (ncRNA)
4. What are the features of ncRNA (non-coding RNA)?

A
  • ncRNA (non-coding RNA) can be encoded by their own genes (RNA) but can also derive from mRNA introns.
  • Most RNA in cells performs catalytic functions: rRNA => 80% of RNA (these RNA form the core of ribosomes).
  • Can be divided into structural/catalytic and regulatory RNAs.
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7
Q

I. Types of RNA and biological importance - Non-coding RNA (ncRNA)
5. What are the 2 types of Non-coding RNA (ncRNA)?

A
  1. Structural / catalytic RNAs
  2. Regulatory RNAs
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8
Q

I. Types of RNA and biological importance - Non-coding RNA (ncRNA)
6B. What are the 5 types of Structural / catalytic RNAs?

A
  1. rRNA (ribosomal RNA)
  2. tRNA (transfer RNA)
  3. snRNA (small nuclear RNA)
  4. snoRNA (small nucleolar RNA)
  5. telomerase RNA
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9
Q

I. Types of RNA and biological importance - Non-coding RNA (ncRNA)
6C. What are the features of rRNA (ribosomal RNA)?

A
  • essential for protein synthesis => the catalytic component of ribosomes
  • synthesized in the nucleolus – from pre-rRNA
  • eukaryotic ribosomes contain 4 different RNA molecules (18S, 5S, 28S, 8S)
  • rRNAs + proteins (nucleoproteins)  ribosome
  • Can be divided into structural/catalytic and regulatory RNAs.
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10
Q

I. Types of RNA and biological importance - Non-coding RNA (ncRNA)
6C. What are the features of tRNA (transfer RNA)?

A
  • carry amino acid to ribosomes
  • contain anticodon (3’-5’) to mRNA which will make up the growing polypeptide chain of protein during translation
  • processed from pre-tRNA
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11
Q

I. Types of RNA and biological importance - Non-coding RNA (ncRNA)
6D. What are the features of snRNA (small nuclear RNA)?

A

function in the removal of the introns from pre-mRNA by RNA splicing

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12
Q

I. Types of RNA and biological importance - Non-coding RNA (ncRNA)
6E. What are the features of snoRNA (small nucleolar RNA)?

A

function in cleavage of the RNA chain and modification of bases during maturation of the rRNA

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13
Q

I. Types of RNA and biological importance - Non-coding RNA (ncRNA)
6F. What are the features of telomerase RNA?

A

Functions in maintaining the sequence at the ends of the chromosomes by working as a template for addition of telomerase

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14
Q

I. Types of RNA and biological importance - Non-coding RNA (ncRNA)
7A. What are the 5 types of Regulatory RNAs?

A
  1. miRNA (microRNA)
  2. siRNA (small interfering RNA)
  3. asRNA (antisense RNA)
  4. Xist-RNA (X-inactive specific transcript RNA)
  5. lncRNA (long non-coding RNA)
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15
Q

I. Types of RNA and biological importance - Non-coding RNA (ncRNA)
7B. What are the features of miRNA (microRNA)?

A
  • Small RNA (22 bases long) which pair mRNA bases extensively
  • this will cause RNA interference, which means it can block the target mRNA from being translated + accelerate its degradation
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16
Q

I. Types of RNA and biological importance - Non-coding RNA (ncRNA)
7C. What are the features of siRNA (small interfering RNA)?

A
  • also small RNA (22 bases long) that interferes RNA in similar way as miRNA
  • difference: siRNA are perfectly complementary to the sequence of an mRNA
    => cause cleavage of the target RNA, leading to rapid degradation
    => siRNA also establish compact chromatin structures
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17
Q

I. Types of RNA and biological importance - Non-coding RNA (ncRNA)
7D. What are the features of asRNA (antisense RNA)?

A

It is ssRNA (single-stranded) complementary to mRNA
=> bind to it
=> block translation

18
Q

I. Types of RNA and biological importance - Non-coding RNA (ncRNA)
7E. What are the features of Xist-RNA (X-inactive specific transcript RNA)?

A

It is a RNA gene on the X-chromosome, which inactive the X-chromosome = bar body

19
Q

I. Types of RNA and biological importance - Non-coding RNA (ncRNA)
7F. What are the features of lncRNA (long non-coding RNA)?

A

It is long structures of RNA (~200 nucleotides) that regulate chromatin structure

20
Q

II. Processing of prokaryotic rRNA and tRNA
1. How is prokaryotic rRNA and tRNA processed?

A
  • Both genes for rRNA and tRNA are clustered in the nucleolus, thus the nucleolus can be thought of as a large factory where noncoding RNAs are being transcribed.
  • All rRNA genes have an important role in forming the nucleolus.
  • After synthesis of mRNA (transcription), the mRNA are ready to start translation.
  • Since translations require both rRNA (to make the ribosomal subunits) and tRNA (make protein), they need to be produced
21
Q

III. Synthesis and maturation rRNA
1. What is the size of eukaryotic ribosome?

A
  • large ribosomal subunit (60S) = 28S, 5S, 5.8S RNA
  • small ribosomal subunit (40S) = 18S RNA
    => total size eukaryotic ribosome = 80S
22
Q

III. Synthesis and maturation rRNA
2. What are the types of eukaryotic rRNA present in each copy per ribosome? What are their features?

A

There are 4 types of eukaryotic rRNA present in each copy per ribosome:
- 18S, 5.8S and 28S are made by chemically modifying and cleaving of single pre-rRNA. The pre-rRNA gene is arranged in a long tandem array. Sequence is from 5’-3’ -> 18S, 5.8S and 28S
- The last rRNA, 5S, is synthesized from a separate cluster of genes by RNA polymerase IIIdoes not require chemical modification

23
Q

III. Synthesis and maturation rRNA
3. What are the 4 steps of rRNA synthesis?

A
  1. Transcription
  2. Chemical modification
    - RNase
    - Direct cleavage
    - Methylation
    - Isomerization
  3. rRNA 5S
  4. rRNA combine with nucleoprotein to form the ribosome
24
Q

III. Synthesis and maturation rRNA
3A. in 4-step of rRNA synthesis, describe the 1. Transcription?

A

Transcription: RNA polymerase binds to the promoter and starts the polymerization
a) In prokaryotes the RNA polymerase synthesize all the RNA in the cell
b) In eukaryotes the RNA polymerase I + III synthesize the ribosomal subunit

25
Q

III. Synthesis and maturation rRNA
3B1. in 4-step of rRNA synthesis, describe the STEP 2: Chemical modification

A

Chemical modification: after synthesis, the rRNA needs to be chemically modified
a) RNase
b) Direct the cleavage
c) Methylation
d) Isomerization

26
Q

III. Synthesis and maturation rRNA
3B2. In 4-step of rRNA synthesis, How does RNase participate in the STEP 2: Chemical modification?

A
  • RNase is an enzyme that cleaves the non-coding sequences
  • These sequences are degraded by exosome associated 3’-5’ nuclear exonucleases (same enzyme which degrade introns spliced from pre-mRNA)
27
Q

III. Synthesis and maturation rRNA
3B3. In 4-step of rRNA synthesis, How does “Direct the cleavage” participate in the STEP 2: Chemical modification?

A
  • snoRNA (small nucleolar RNA) and sn RNPs (small
    nuclear ribonucleoproteins) position themselves on the pre-RNA, and thereby bringing the RNA modifying enzymes to the appropriate position.
  • Other snoRNAs aid cleavage of pre-rRNA into mature rRNA by exposing site of nucleases
28
Q

III. Synthesis and maturation rRNA
3B4. In 4-step of rRNA synthesis, How does “Methylation” participate in the STEP 2: Chemical modification?

A

methylation of the 2’-OH position on nucleotide sugars

29
Q

III. Synthesis and maturation rRNA
3B5. In 4-step of rRNA synthesis, How does “Isomerization” participate in the STEP 2: Chemical modification?

A

Isomerization (transforming a substance into an isomer
- isomerization of uridine nucleotides to pseudouridine

30
Q

III. Synthesis and maturation rRNA
3C. In 4-step of rRNA synthesis, describe step 3 “rRNA 5S”.

A
  • rRNA 5S: encoded separately and transcribed outside the nucleolus in the nucleoplasm by RNA polymerase III.
  • With minor additional processing to remove nucleotides at the 3’-end, it diffuses to the nucleolus, where it assembles with other rRNA
31
Q

III. Synthesis and maturation rRNA
3D. In 4-step of rRNA synthesis and maturation, describe LAST STEP!

A

The products are 2 ribosomal subunits in the nucleolus which diffuse via the nuclear pores into the cytosol, where the rRNA combine with nucleoprotein to form the ribosome
=> ready for use in translation

32
Q

III. Synthesis and maturation rRNA
4. What are Cajal bodies (nuclear bodies) ?

A

Cajal bodies (nuclear bodies) = subnuclear structures, sites where components involved in RNA processing are assembled, sorted and recycled.

33
Q

IV. Synthesis of tRNA
1. What are the features of tRNA?

A
  • tRNA (80 nucleotides in length) has a key function in translation.
  • Cleavage and base modification occur during processing of all pre-tRNA (some pre-tRNA are also spliced during processing)
  • Processing occurs in the nucleus
34
Q

IV. Synthesis of tRNA
2. How is tRNA synthesized?

A
  1. Transcription: RNA polymerase III synthesizes tRNA (pre-tRNA) in nucleoplasm
  2. Splicing: cut off 5’ and 3’ end of pre-tRNA by endonucleases
    a) In eukaryotes, RNase P (nuclear ribonuclease P) cleaves the 5’end of pre-tRNA
    b) In prokaryotes, RNase D (nuclear ribonuclease D – exonuclease!) cleaves the 3’ end
  3. Introns splicing: removal of introns in some tRNA
    - Splicing occurs by a ‘’cut-and-paste’’ mechanism catalyzed by proteins
    - Splicing and intron splicing (step 2 + 3) require the pre-tRNA to be correctly folded in
    its clover leaf configuration
35
Q

IV. Synthesis of tRNA
3. What are the enzyme and location for tRNA synthesis?

A

RNA polymerase III synthesizes tRNA (pre-tRNA) in nucleoplasm

36
Q

IV. Synthesis of tRNA
3. How does splicing occur in tRNA synthesis in prokaryote and eukaryote?

A

Splicing: cut off 5’ and 3’ end of pre-tRNA by endonucleases
- In eukaryotes, RNase P (nuclear ribonuclease P) cleaves the 5’end of pre-tRNA
- In prokaryotes, RNase D (nuclear ribonuclease D – exonuclease!) cleaves the 3’ end

37
Q

IV. Synthesis of tRNA
4. How does intron splicing occur in tRNA synthesis?

A

Introns splicing: removal of introns in some tRNA
- Splicing occurs by a ‘’cut-and-paste’’ mechanism catalyzed by proteins
- Splicing and intron splicing (step 2 + 3) require the pre-tRNA to be correctly folded in
its clover leaf configuration

38
Q

V. Maturation of tRNA
1. How does tRNA maturation occur?

A

3 classes of covalent base modifications occur in pre-tRNA and are necessary for the tRNA to be transported to the cytosol and used in protein synthesis:
1. CCA sequence replace U-residues at 3’end of pre-tRNA by tRNA nucleotidyl transferase. The CCA sequence covalently attaches to amino acid by aminoacyl tRNA synthetases.
2. Methyl + isopentenyl groups are added to heterocyclic ring of purine bases. The 2’- OH groups of ribose is methylated
3. Specific uridines are converted to dihydrouridine, pseudouridine or ribothymidine residues
- After pre-tRNAs are processed in the nucleus, the mature tRNA are transported to the cytoplasm through the nuclear pore complex by exportin-t + exportin  ready for protein translation

39
Q

V. Maturation of tRNA
2. What are the 3 classes of covalent base modifications that occur in pre-tRNA and are necessary for the tRNA to be transported to the cytosol and used in protein synthesis?

A
  1. CCA sequence replace U-residues at 3’end of pre-tRNA by tRNA nucleotidyl transferase. The CCA sequence covalently attaches to amino acid by aminoacyl tRNA synthetases.
  2. Methyl + isopentenyl groups are added to heterocyclic ring of purine bases. The 2’- OH groups of ribose is methylated
  3. Specific uridines are converted to dihydrouridine, pseudouridine or ribothymidine residues
40
Q

V. Maturation of tRNA
3. How is the pre-tRNA processed and transported?

A

After pre-tRNAs are processed in the nucleus, the mature tRNA are transported to the cytoplasm through the nuclear pore complex by exportin-t + exportin
=> ready for protein translation

MCB 2 (59 decks)

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