The process that produces a complementary strand of RNA from a section of DNA or (rarely) other RNA.

learn more… | top users | synonyms

10
votes
1answer
224 views

Why and how is DNA synthesis so much faster then RNA synthesis in bacteria?

DNA synthesis in E. coli is 20x faster than RNA synthesis at 1000nt/s vs 50nt/s. (Mirkin'05) I find that perplexing since DNA polymerization has better proofreading than the RNA variety, which ...
1
vote
2answers
65 views

Relationship between DNA strands and mRNA

Does the sense strand or antisense strand of DNA code for the polypeptide product? I'm confused because I know the antisense strand is the template for mRNA but it has anti codons so I do not know how ...
3
votes
3answers
669 views

Why isn't there a standard unit of promoter strength?

Sometimes in synthetic biology, we need to know rates of transcription of one promoter in relation to others (particularly inducible vs constitutive) in order to perform tasks like balancing ...
0
votes
0answers
15 views

Does prokaryotic transcription have activators / enhancer regions involved?

I am designing a biosensor, and I need to know whether prokaryotic transcription involves or can involve (if a gene needs to be regulated) enhancer regions. Also, where are enhancer regions located (...
1
vote
1answer
66 views

What is the “transcriptome” in layman's term?

I am new to the bioinformatics field and am trying to understand a research paper that includes some definitions which I looked up on the internet, but couldn't find the proper definition of following:...
3
votes
1answer
19 views

How would one determine whether a chemical will upregulate a certain class of proteins?

I'm trying to determine whether certain organic chemicals will upregulate classes of proteins that possess deacylase activity.  How would I go about this experiment? I'm assuming I would use some ...
0
votes
2answers
69 views

Multiple start and stop codons in mRNA and pre-mRNA [duplicate]

I have a main question that will lead to further questions depending upon the answer. In the process of transcription, will there be multiple start and stop codons in one sequence of pre-mRNA? If ...
20
votes
2answers
1k views

How does RNA transcription determine which half of the DNA to use?

I feel that I might have a complete misunderstanding here. If DNA has two strands, how does the machinery of RNA transcription determine which one to transcribe?
3
votes
1answer
55 views

Is there selection against long proteins and long genes?

Background thought Titin and TTN Titin is the largest protein in the human genome with 33423 amino acids. Titin is coded by the gene TTN that must be at least $3 \cdot 33423 \approx 100kb$ long. ...
4
votes
0answers
44 views

How do chromosome pairs get “paired up” for protein synthesis?

If my understanding is correct, during interphase a normal human cell will have 46 chromosomes scattered about in the cell nucleus. These chromosomes can be thought of as pairs: there are two copies ...
4
votes
3answers
100 views

Do transcripts always start and end with exons?

I realized that in all cases of "RefSeq Genes" annotations of hg19 I looked at spliced transcripts start (and end) with an exon. From the annotation there is no evidence of any sequence upstream or ...
1
vote
1answer
41 views

Deducing amino acid sequence from a DNA sequence

The suggested answer to the question is the following: "M L S C D K S D Stop". I do not understand how they get that result. The question is as follows: An RNA polymerase transcribes the following ...
2
votes
3answers
106 views

Relationship of the DNA of a eukaryotic gene to the 5'-UTR of its mRNA

In eukaryote pre-mRNA I am having a little trouble grasping exactly what the 5 prime untranslated region is defined as. It seems that it could be defined as the difference in pre-mRNA between the ...
1
vote
2answers
48 views

difference between transcriptional activator and general transcription factors?

What is the difference between transcriptional activator and general transcription factors? Are they same or different, and do the transcriptional activators first attract general transcription ...
2
votes
3answers
201 views

Why don't housekeeping genes have TATA Box regions in their promoter sequences?

Housekeeping genes are genes that are continuously transcribed. Like all other genes they have promoter sequences, but they don't have TATA box sequences that are used to specify from where ...
1
vote
0answers
28 views

Hydrogen bonding and the blocking thereof in nucleic acids during nuclear processes

In transcription, RNA polymerase unwinds the DNA double helix and begins attaching RNA nucleotides to the template strand. In its wake, the DNA double helix closes back—this is only natural, seeing as ...
0
votes
0answers
22 views

Cytokine screening

I am measuring IL-6 production by NF-κB stimulation using IL-1α and TNFα. Il-1 produces a stronger degradation of IκBα (inhibitor of NF-κB). I've done this using ...
2
votes
1answer
113 views

Why is there no U3 snRNP in the spliceosome complex of transcription initiation?

snRNP U1,U2,U4,U5,U6 are present in the spliceosome but there is no mention of U3.
1
vote
2answers
49 views

identifying which SNPs sit in TFBS (Yeast)

i have a set of ~11k SNPs for Saccharomyces cerevisiae, baker's yeast and i would like to identify which ones of these sit in transcription factor binding sites and if they do information on the ...
1
vote
0answers
33 views

Is DNA transcription inactive during mitosis ie no proteins are made? How does the cell survive?

I've read that during mitosis, DNA exists as heterochromatin, a form that is unable to be accessed for transcription. Does this mean no new proteins are made during what can be 20% of a cell's life? ...
1
vote
1answer
127 views

TSS of a gene vs TSS of a transcript

I have an annotation from gencode.vM1.annotation of a mouse. Exons, genes, transcripts and UTR are listed there. For each feature a start and end positions are present. I need to find a TSS for each ...
2
votes
2answers
106 views

TFBS predictions for yeast and pombe?

Are there any resources out there for TFBS (transcription factor binding site) predictions for the yeast (S. cerevisiae) and S. pombe genomes? Even if these are only de novo predictions, I would like ...
0
votes
1answer
32 views

Time needed for transcription of DNA [closed]

How much time would it take to complete the transcription of an average-sized human gene?
0
votes
1answer
66 views

How does RNA polymerase achieve higher processivity?

DNA polymerase uses a sliding clamp in order to replicate DNA. RNA polymerase does not require one. What allows RNA polymerase to hold on to DNA just like DNA polymerase?
1
vote
1answer
36 views

Transcription of Genes: Are Specific Transcription Factors + Enhancers Necessary?

I learned about transcription in my AP Biology class and we discussed how transcription occurs, but I was wondering whether transcription always requires the enhancers, activators (specific ...
2
votes
1answer
1k views

ATP required for cell processes [closed]

I haven't been able to find anything that tells me how much ATP is needed for DNA replication, transcription, and translation in humans, just papers that mention ATP used in those processes. I need ...
1
vote
0answers
15 views

Are both chromosomes transcribed and translated? [duplicate]

Or is it somehow regulated if both or only one chromosome is transcribed/translated?
0
votes
2answers
45 views

General transcription factors vs. DNA Binding transcription factors

I know that DNA binding transcription factors are trans-acting, but what about general transcription factors? Are they cis or trans acting?
0
votes
0answers
40 views

What is the difference between basal transcription and activated transcription?

My professor keeps mentioning these two forms of transcription and I'm completely confused as to what the difference is between them. I didn't even realise there were two different types of ...
0
votes
1answer
34 views

Transcription when Chromosomes are Condensed

Are genes transcribed just as well when chromosomes are condensed? I want to design a screen that depends on genes not transcribed when chromosomes are condensed (to identify cells that can't ...
0
votes
0answers
17 views

How many Stress Response Transcription Factors are there in yeast (and what are they)

I've Read that there are ~209 TFs in Yeast, but I'd like to know how many (and which) of these TFs are associated with Stress Responses? Is there a paper someone can link me to?
3
votes
1answer
148 views

How do eukaryotes terminate transcription? (clarification on Campbell Biology)

I'm having trouble understanding how eukaryotes terminate transcription. Studying Campbell Biology (pg. 342, 10th ed.), I read: In eukaryotes, RNA polymerase II transcribes the polyadenylation ...
1
vote
1answer
268 views

How do DNA-binding proteins determine that they're binding to the correct DNA base pairs?

My professor posed this question to the class today - "How do DNA binding proteins specifically bind to base pairs?" He alluded to the different arrangements of hydrogen-bond donor and acceptors in A-...
1
vote
0answers
23 views

Will bacterial promoter without either -10 or -35 sequence allow no transcription?

I have a strong constitutive promoter on a plasmid inside of E.Coli, which expresses a gene. Having either -10 or -35 sequence modified to random sequence, will it ensure zero transcription from that ...
1
vote
1answer
50 views

How does the MET gene work and what happens when the promoter region gets mutated?

I am doing research on inherited risk of Autism Spectrum Disorders(ASD) due to common Copy Number Variants(CNVs) One of the mutations is the 'CC' variant of Rs1858830 in the promoter region of the MET ...
1
vote
1answer
14 views

What was the first gene(s) found to code for ncRNA

I could not find a source that states what the first gene found to code for ncRNA was. Someone told me, however, it was a gene that coded for either rRNA or tRNA. To this point in time I have had no ...
2
votes
0answers
91 views

Multiple transcripts encoding for one protein

Trying to get a better understanding of the process of DNA to proteins. So when we have a gene, it is read from the 5' to 3' end, only translating the exons to mRNAs. A single gene can have multiple ...
0
votes
0answers
21 views

translation rate regulated by transcription factors?

I'd like to know if there is in the litterature some examples of transcription factors capable to impact not just transcription but also translation rate so that both can be adjusted. I would be very ...
1
vote
1answer
195 views

What is the spacing between stop codon and transcription terminator?

When one tries to express a protein from a synthetic plasmid in E. coli, how many base pairs should there be between stop codon and the transcription terminator site?
6
votes
3answers
830 views

Mutation That Loses Stop Codon

Someone asked this in my class and my instructor wasn't sure in her answer, doesn't anyone know what happens in protein synthesis if a mutation causes mRNA to not possess a stop codon? Would the ...
3
votes
0answers
19 views

Gene silencing: relative or absolute number of methylated CpG sites?

CpG content varies a lot across the human genome. What does determine a promoter to be silenced through DNA methylation: the fraction of CpG sites that are methylated or the total number of methylated ...
3
votes
1answer
32 views

Is RNA polymerase affected by proteins bound to the coding sequence of a gene?

I am designing a synthetic gene construct to express genes in E. coli driven by either Ptet or PLacO. The construct would look like: -Ptet-(Gene1)-PLacO-(Gene2)- I want to express each gene using ...
1
vote
0answers
27 views

Are upstream activating factor (UAF) and upstream binding factor (UBF) the same thing?

During ribosome pre-40S and pre-60S synthesis, many sources state the importance of UAF or UBF in initiation complex of ribosome DNA transcription. None of the sources I've seen mentions the other ...
1
vote
2answers
3k views

Stop codons and exons?

If we had a hypotheical gene called gene exampleGene and this gene had 5 exons, labeled A, B, C, D, and E in that order on the chromosome, could it be the case that the stop codon for this gene be on ...
6
votes
2answers
106 views

How predictably will RNA polymerase not transcribe repetitive sequences?

I am working on an (expensive) synthetic construct, which happens to have many "repetitive" sequences within it that are integral to its function. Primarily, the two sequences that are worrying me are:...
12
votes
2answers
228 views

Modularity of transcription factors

I attended a seminar about neurogenesis that presented results for PAX6 as an important TF that contains 3 domains with very distinct patterns of downstream expression. The speaker ended up saying ...
5
votes
2answers
84 views

Why is 5S-rRNA is different from other rRNAs in place of transcription and usage of RNA polymerase?

While transcription of rRNAs happens in nucleolus mediated by RNA Polymerase-I, we see that 5S-rRNA is transcribed elsewhere by RNA Polymerase-III. What is the cause and why?
5
votes
1answer
83 views

Location of TFBS in genome

I have an annotated set of SNPs and I would like to explore the difference in the binding affinity of the transcription factor (TF) if I have a SNP in my locus. As my SNPs are annotated (I know wether ...
3
votes
2answers
90 views

RNA polymerase question

In this question we are examining a bacterial RNA polymerase that elongates at 20 codons per second. Question 1: How long will this RNA polymerase take to transcribe the Lac Z gene at 3510 base pairs? ...