Term
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Definition
| Initial RNA polymerase and factor binding region on the template DNA |
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Term
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Definition
DNA directed RNA synthesis is catalyzed by RNA polymerase.
Multi-subunit enzyme, and
σ
70
subunit dissociates from the core polymerase after binding to
DNA. |
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Term
Initiation sites have unique DNA sequences called promoter which is recognized by σ-factor.
. |
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Definition
1. -10-bp (Pribnow box) has TATAAT consensus sequence.
2. -35-bp region has TTGACA consensus sequence.
3. The initiation sites are either A or G (purine sequence). |
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Term
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Definition
1. Holoenzyme binds very tightly (K
d = 10 ^(-12)M to the promoter.
2. RNA synthesis is immediately started (Elongation direction is 5’
→ 3’ direction).The substrates are ATP, GTP, CTP, and UTP, and PPi is one of products.
Substrate hydrolysis provides synthesis energy.
3. After 10 nucleotides are added, σ
-factor is dissociated from the enzyme.
4. RNA polymerase under- and over-winds DNA at the behind and ahead of transcription
bubble, respectively. Thus the nascent RNA is straight line. Topoisomerase I and II relax the supercoiled DNA |
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Term
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Definition
Rifamycin binds to β subunit and prevents 2nd diester bond formation (i.e., it prevents
further chain elongation). |
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Term
| cardycepin (3’-Deoxyadenosine) |
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Definition
stops elongation, because no 3’-OH. Note: 3’-
Deoxyadenosine does not have PPP, but the PPP is attached PPP after entering a cell, which
provides energy for the chain elongation reaction |
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Term
| actinomycin D and daunomycin |
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Definition
intercalate into DNA and inhibit RNA
polymerase.
Phenoxazone ring intercalates between two base-pairs, specifically 5’-GC-3’.
We confirmed the intercalation of actinomycin D into DNA by an X-ray diffraction method. |
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Term
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Definition
There are two ways to proceed RNA synthesis along the template DNA.
- Positive supercoiling ahead of transcription bubble which is relaxed by Topo II (gyrase).
- Negative supercoiling behind of transcription bubble which is relaxed by Topo I. |
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Term
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Definition
Sequence termination: GC rich palindrome sequence followed by 4~10 T sequence in
DNA.
The palindrome section of RNA forms a hairpin structure which induces the
conformational changes in RNA polymerase. Thus, the RNA is released. |
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Term
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Definition
2.ρ-factor termination: Protein
ρ-factor travels with RNA polymerase, and at the pause site
(GC -rich palindrome sequence which allow the RNA to form a hairpin structure),
ρ-factor induces termination of the synthesis. |
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Term
| Eukaryotic RNA polymerases I |
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Definition
- is located in nucleolus.
- makes pre-rRNA.
- is α-amanitin resistant (i.e., is not inhibited by α-amanitin).
Note: α-amanitin is an antibiotic found in fatal mushroom poisonings. |
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Term
| Eukaryotic RNA polymerases II |
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Definition
- is located in nucleoplasm.
- makes hnRNA (pre-mRNA) Note: hn = heterogeneous nuclear.
- is α-amanitin sensitive (i.e., is inhibited by α-amanitin). |
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Term
| Eukaryotic RNA polymerases III |
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Definition
- is located in nucleoplasm.
- makes pre-tRNA, 5S rRNA.
- is α-amanitin sensitive at high drug concentration level.
- Polymerases in mitochondria and chloroplast are quite different from those in nucleus. |
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Term
| RNA polymerase I promoters |
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Definition
- Each RNA polymerase I only recognizes one promoter.
- RNA polymerase promoters are species specific.
- RNA polymerase promoters are located: -186 to +6 on the template strand.
- Core promoter element: -31 to +6.
- Upstream promoter element: -187 to -107. |
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Term
| RNA polymerase II promoters |
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Definition
- The constitutive genes have GC box (GGGCGG consensus sequence) in their promoters
- The structural genes have TATA box (TATATAATA sequence) in their promoters.
- are located-25 to -30 on the DNA template strand.
• RNAPII promoters:
- are located at downstream, +40 to +80 on the DNA template strand. |
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Term
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Definition
- are inducible transcription factor binding sites on the DNA template.
- have specific sequences.
- Without enhancer, RNA synthesis rate is reduced as much as 10^9times. |
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Term
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Definition
recognize the promoter (initiation site) and deliver RNAPII to it. They form a pre-initiation complex
(PIC) with RNAPII |
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Term
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Definition
--- bind to specific DNA sequences at upstream of the initiation site, and
stimulate or repress the transcription initiation (PIC). They recognize both DNA and PIC. |
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Term
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Definition
--- are activated by phosphorylation or by a specific ligand binding, and then
bind to specific DNA sequences at upstream of the initiation site, and stimulate or repress the transcription initiation (PIC). Example: steroid receptors. |
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Term
| Transcription factors have unique structural motifs |
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Definition
1. Zinc finger DNA-binding motifs --- Amino acid sequence contains (··Cys-Cys·····His-
His··)n repeats. A Zn2+ iscoordinated by 2 Cys and 2 His.
2. Leucine zippers --- Amino acid sequence contains 7-residue pseudo-repeat (a-b-c-d-e-f-g)n |
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Term
| Posttranscriptional Processing |
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Definition
1. Appending nucleotide sequences to their 3’ and 5’ ends.
2. Removal of polynucleotide segments by exo and endonucleases.
3.Modification of specific nucleotides. |
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Term
| Eukaryotic mRNA processing |
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Definition
The 5’-end is capped by 7-methylguanosine via 5’-5’ triphosphate bridge.
2. A poly(A)n, (n = 20~50) tail is appended to the 3’-end.The poly(A) tail protects the RNA against degradation by RNases.
3. Removal of intervening sequences. mRNA primary transcripts are composed of
intron and exon regions. The intron sections must be removed to form a mature mRNA by
3 splicing reactions. |
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Term
.Splicing reaction
• mRNA |
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Definition
1. Introns contain consensus sequences for splicing. 5’-GU···CURAY···AG-3’
where R (purine) = A or G;Y(pyrimidine) = C or U.
2. The 2’-OH of A in CURAY attacks 5’-phosphate of 5’-G to form 2’,5’-lariat structure.
3. The liberated 3’-OH of the exon attacks the phosphate of the 5’-terminal residue of the
next exon. The intron is cut off, and two exons are connected to each other |
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Term
| .Splicing reaction snRNPs |
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Definition
(small nuclear RNA complexed with proteins) facilitate the RNA splicing
reactions. |
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Term
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Definition
| No intron in prokaryotes and very few intron in eukaryotes. |
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Term
| Prokaryotes Ribosomal RNA (rRNA) |
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Definition
1. One primary transcript contains 23S, 16S, 5S rRNAs, and some tRNAs with spacers.
2. These RNAs are cut out by various RNases. |
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Term
Eukaryotes Ribosomal RNA
: |
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Definition
1. The primary transcript, 45S rRNA, contains 18S, 5.8S, and 28S rRNAs with spacers.
2. rRNAs are cut out by RNases, and introns are eliminated by self-splicing mechanism.
3. Self-splicing mechanism:
• The 3’-OH of a free guanosine cleaves the phosphodiester bond of the 3’-end of left exon.
• The liberated 3’-OH of the left exon attacks the 5’-end phosphate of the right exon. The
intron is cleaved, and the two exons are coonected.
• The cleaved intron is further spliced into two pieces. |
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Term
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Definition
• Self-splicing function of RNA indicates that some RNAs have an enzyme activity.
• Small hammerhead RNAs have indeed nuclease activities that cleave a single strand DNA. These RNAs are called ribozymes
. |
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Term
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Definition
Primary transcript (pre-tRNA) contains two introns at both 5’- and 3’-ends.
• After folding into a cloverleaf structure, the introns are cleaved by RNase P and F, respectively.
• The accepting arm 3’-ACC is attached to the 3’-end.
• Base modifications take place after splicing. |
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Term
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Definition
• Pre-tRNA is immediately folded into a cloverleaf structure.
• 19-nucleotides at 5’-end are cleaved.
• The accepting arm 3’-ACC is attached to the 3’-end.
• 14-nucleotides intervening sequence in the anticodon arm is removed and ligated to yield a
mature tRNA. |
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Term
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Definition
tRNA has a cloverleaf secondary structure, which contains three stem loops (called D arm,
The tip of the anticodon arm has an anticodon (XYZ), and the 3’-terminal is a single strand
with sequence of -CCA-OH where an amino acid is attached.
anticodon arm, and T ψ C arm), a small arm (variable arm), and accepting stem. |
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