I. DNA & RNA| 12. Characterization, role and synthesis of different types of RNA Flashcards
What are the general structure and function of RNA?
- 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
I. Types of RNA and biological importance
1. What are 2 types of protein-coding RNA?
- mRNA (messenger RNA)
- pre-mRNA
I. Types of RNA and biological importance - Protein-coding RNA
2. What are the features of mRNA (messenger RNA)?
- 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
I. Types of RNA and biological importance - Protein-coding RNA
2. What are the features of pre-mRNA?
- precursor of mRNA = not processed mRNA yet
- with introns, but without 5’-cap and poly-A tail
I. Types of RNA and biological importance - Protein-coding RNA
3. What does hnRNA (heterogenous nuclear RNA) include?
hnRNA (heterogenous nuclear RNA) includes the pre-mRNA and the RNA- processing intermediates which contain 1 or more introns
I. Types of RNA and biological importance - Non-coding RNA (ncRNA)
4. What are the features of ncRNA (non-coding RNA)?
- 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.
I. Types of RNA and biological importance - Non-coding RNA (ncRNA)
5. What are the 2 types of Non-coding RNA (ncRNA)?
- Structural / catalytic RNAs
- Regulatory RNAs
I. Types of RNA and biological importance - Non-coding RNA (ncRNA)
6B. What are the 5 types of Structural / catalytic RNAs?
- rRNA (ribosomal RNA)
- tRNA (transfer RNA)
- snRNA (small nuclear RNA)
- snoRNA (small nucleolar RNA)
- telomerase RNA
I. Types of RNA and biological importance - Non-coding RNA (ncRNA)
6C. What are the features of rRNA (ribosomal RNA)?
- 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.
I. Types of RNA and biological importance - Non-coding RNA (ncRNA)
6C. What are the features of tRNA (transfer RNA)?
- 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
I. Types of RNA and biological importance - Non-coding RNA (ncRNA)
6D. What are the features of snRNA (small nuclear RNA)?
function in the removal of the introns from pre-mRNA by RNA splicing
I. Types of RNA and biological importance - Non-coding RNA (ncRNA)
6E. What are the features of snoRNA (small nucleolar RNA)?
function in cleavage of the RNA chain and modification of bases during maturation of the rRNA
I. Types of RNA and biological importance - Non-coding RNA (ncRNA)
6F. What are the features of telomerase RNA?
Functions in maintaining the sequence at the ends of the chromosomes by working as a template for addition of telomerase
I. Types of RNA and biological importance - Non-coding RNA (ncRNA)
7A. What are the 5 types of Regulatory RNAs?
- miRNA (microRNA)
- siRNA (small interfering RNA)
- asRNA (antisense RNA)
- Xist-RNA (X-inactive specific transcript RNA)
- lncRNA (long non-coding RNA)
I. Types of RNA and biological importance - Non-coding RNA (ncRNA)
7B. What are the features of miRNA (microRNA)?
- 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
I. Types of RNA and biological importance - Non-coding RNA (ncRNA)
7C. What are the features of siRNA (small interfering RNA)?
- 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
I. Types of RNA and biological importance - Non-coding RNA (ncRNA)
7D. What are the features of asRNA (antisense RNA)?
It is ssRNA (single-stranded) complementary to mRNA
=> bind to it
=> block translation
I. Types of RNA and biological importance - Non-coding RNA (ncRNA)
7E. What are the features of Xist-RNA (X-inactive specific transcript RNA)?
It is a RNA gene on the X-chromosome, which inactive the X-chromosome = bar body
I. Types of RNA and biological importance - Non-coding RNA (ncRNA)
7F. What are the features of lncRNA (long non-coding RNA)?
It is long structures of RNA (~200 nucleotides) that regulate chromatin structure
II. Processing of prokaryotic rRNA and tRNA
1. How is prokaryotic rRNA and tRNA processed?
- 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
III. Synthesis and maturation rRNA
1. What is the size of eukaryotic ribosome?
- large ribosomal subunit (60S) = 28S, 5S, 5.8S RNA
- small ribosomal subunit (40S) = 18S RNA
=> total size eukaryotic ribosome = 80S
III. Synthesis and maturation rRNA
2. What are the types of eukaryotic rRNA present in each copy per ribosome? What are their features?
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 IIIdoes not require chemical modification
III. Synthesis and maturation rRNA
3. What are the 4 steps of rRNA synthesis?
- Transcription
- Chemical modification
- RNase
- Direct cleavage
- Methylation
- Isomerization - rRNA 5S
- rRNA combine with nucleoprotein to form the ribosome
III. Synthesis and maturation rRNA
3A. in 4-step of rRNA synthesis, describe the 1. Transcription?
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
III. Synthesis and maturation rRNA
3B1. in 4-step of rRNA synthesis, describe the STEP 2: Chemical modification
Chemical modification: after synthesis, the rRNA needs to be chemically modified
a) RNase
b) Direct the cleavage
c) Methylation
d) Isomerization
III. Synthesis and maturation rRNA
3B2. In 4-step of rRNA synthesis, How does RNase participate in the STEP 2: Chemical modification?
- 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)
III. Synthesis and maturation rRNA
3B3. In 4-step of rRNA synthesis, How does “Direct the cleavage” participate in the STEP 2: Chemical modification?
- 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
III. Synthesis and maturation rRNA
3B4. In 4-step of rRNA synthesis, How does “Methylation” participate in the STEP 2: Chemical modification?
methylation of the 2’-OH position on nucleotide sugars
III. Synthesis and maturation rRNA
3B5. In 4-step of rRNA synthesis, How does “Isomerization” participate in the STEP 2: Chemical modification?
Isomerization (transforming a substance into an isomer
- isomerization of uridine nucleotides to pseudouridine
III. Synthesis and maturation rRNA
3C. In 4-step of rRNA synthesis, describe step 3 “rRNA 5S”.
- 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
III. Synthesis and maturation rRNA
3D. In 4-step of rRNA synthesis and maturation, describe LAST STEP!
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
III. Synthesis and maturation rRNA
4. What are Cajal bodies (nuclear bodies) ?
Cajal bodies (nuclear bodies) = subnuclear structures, sites where components involved in RNA processing are assembled, sorted and recycled.
IV. Synthesis of tRNA
1. What are the features of tRNA?
- 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
IV. Synthesis of tRNA
2. How is tRNA synthesized?
- Transcription: RNA polymerase III synthesizes tRNA (pre-tRNA) in nucleoplasm
- 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 - 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
IV. Synthesis of tRNA
3. What are the enzyme and location for tRNA synthesis?
RNA polymerase III synthesizes tRNA (pre-tRNA) in nucleoplasm
IV. Synthesis of tRNA
3. How does splicing occur in tRNA synthesis in prokaryote and eukaryote?
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
IV. Synthesis of tRNA
4. How does intron splicing occur in tRNA synthesis?
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
V. Maturation of tRNA
1. How does tRNA maturation occur?
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
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?
- 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.
- Methyl + isopentenyl groups are added to heterocyclic ring of purine bases. The 2’- OH groups of ribose is methylated
- Specific uridines are converted to dihydrouridine, pseudouridine or ribothymidine residues
V. Maturation of tRNA
3. How is the pre-tRNA processed and transported?
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
