Term
| What is a stem loop in prokaryotic RNA? |
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Definition
| Stem loops, or hairpin structures, are important secondary organization structures formed in RNA by Watson-Crick base pairing. |
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Term
| True or False: More transcript processing occurs in prokaryotic RNA synthesis than in eukaryotic RNA synthesis. |
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Definition
| False - more occurs in eukaryotic RNA synthesis. |
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Term
| How does the tuberculosis drug Rifampin affect RNA synthesis in mycobacteria? |
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Definition
| It binds the beta subunit of bacterial RNA polymerases and prohibits exit of the RNA transcript from the exit channel. Therefore, mycobacteria are unable to synthesize RNAs or proteins necessary for survival. |
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Term
| What are the 3 types of RNA coded for by DNA-dependent RNA polymerase in prokaryotes? |
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Definition
1) messenger (mRNA) - the template that codes for protein amino acids
2) ribosomal (rRNA) - RNAs that complex with proteins to form ribosomes for protein synthesis
3) transfer (tRNA) - small RNAs that act as adapter molecules, linking amino acids to nucleic bases |
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Term
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Definition
Initiation: 1-3
Abortive Initiation: 3 (goes back to 1)
Elongation: 4-5
Termination: 6-7 |
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Term
| True or False: Prokaryotic RNA synthesis requires a primer. |
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Definition
| False - RNA synthesis doesn't require a primer in prokaryotes. |
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Term
| What are the 4 requirements of RNA polymerase to complete prokaryotic RNA synthesis? |
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Definition
1) A DNA template to transcribe into RNA.
2) Ribonucleotides: ATP, GTP, UTP, CTP. No deoxynucleotides.
3) Divalent cation, either Mg+2 or Mn+2.
4) Sigma factor, which scans the DNA code to find transcriptional start sites. |
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Term
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Definition
| These are A-T rich regions about 10 bp into the DNA sequence, similar to TATA boxes in humans. Sigma factor recognizes this as part of a promoter, along with a second site at 35 bp. Individual sequences will vary to have strong or weak promoters. |
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Term
| What are consensus sequences? Give an example. |
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Definition
| Pribnow boxes are an example of consensus sequences; these are the nucleotides most frequently found in comparing many real sequences. Individual sequences, however, may vary. |
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Term
| True or False: Multiple copies of a gene can be made simultaneously by RNA polymerase in prokaryotes. |
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Definition
| True - the polymerase will read 5' to 3' and multiple copies can be made at once. |
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Term
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Definition
| The 3' end is on the left, since transcription occurs in a 5' to 3' direction and the RNA strands closer to the 5' end would have had longer to form and polymerize, therefore being longer strands. |
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Term
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Definition
| The black "dots" are where the rRNA has begun to form secondary structure (stem loops) while synthesis is still ongoing in the nascent strand. |
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Term
| True or False: RNA synthesis copies both strands of the DNA. |
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Definition
| False - RNA synthesis copies only one DNA strand so that the RNA sequence is complementary to this template strand. |
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Term
| In what direction does RNA synthesis occur? |
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Definition
| Synthesis occurs in the 5' to 3' direction. |
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Term
| Why is RNA synthesis considered low-fidelity copying? |
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Definition
| Since there is no 3' to 5' proofreading exonuclease activity, synthesis is considered low-fidelity. |
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Term
| True or False: Only Watson-Crick base pairing governs the secondary structure of RNA molecules. |
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Definition
| False - nonconventional base pairs can form to create complex 3D structures, like the ribosome. |
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Term
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Definition
| In bacteria, an operon is a cluster of genes transcribed as a single mRNA molecule. An example is the Trp operon, a repressable operon used to make tryptophan. |
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Term
| What happens when there is excess tryptophan in a bacterial cell? |
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Definition
| The tryptophan binds a protein that binds to the operator sequence (part of the promoter region) of the trp operon and inhibits transcription of the gene. |
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Term
| True or False: Amplification does not occur in RNA synthesis (transcription). |
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Definition
| True - unlike proteins, ribosomes are made directly from rRNA transcripts, so no amplification may occur. |
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Term
| Why are there multiple copies of rRNA genes in bacterial DNA? |
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Definition
| This allows for multiple ribosomes to be synthesized at once, which is necessary for high rates of protein synthesis. |
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Term
| What is sigma factor 32? When is it released? |
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Definition
| Sigma factor 32 is released when bacteria are subjected to stressful conditions, such as high temperature. This factor is used to transcribe special genes for the stress conditions in a process known as the Heat Shock Response or Stress Response. |
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Term
| In the Cystic Fibrosis case study, what was the effect of upregulation of rpoH (a sigma-32 homolog) on patient health? |
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Definition
| This promoted the mucoid phenotype (bad!) of the Pseudomonas infection and basically worsened the patient prognosis. |
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