Questions tagged [molecular-genetics]

The scientific study of the structure and function of genes at the molecular level, particularly chromosomes and DNA.

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What is the current molecular explanation of Mendel's pea cross?

With reference to the simplest Punnet square for Mendel's pea plant experiments it occurred to me that I could not connect the little I know about genetics to the little I know about molecules. The ...
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Do cell walls prevent cancer?

To my knowledge plants do not have an uncontrolled growth disease similar to cancer. Is the function by which they avoid uncontrolled growth related to their cell wall and preventing damage to DNA/RNA?...
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Is it reasonable to assume that RNA polymerase would bind preferentially to the promoter of the long allele of the SERT gene?

I'm trying to come up with an idea for a school project (a hypothetical research study). I'm looking at depression and the serotonin transporter gene, which is highly expressed in the human ...
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How does GC-content evolve?

Background GC-content refers to the frequency of base pairs that are either C or G in the genome, or in other words the number of GC base pairs divided by the addition of the number of GC base pairs ...
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Sexual Differentiation in Monoecious plants with unisexual flowers

In monoecious plants having unisexual flowers (eg Zea Mays, Ricinus Communis etc), there must be some mechanism as to produce two sexually distinct flowers from the same genotype. Since both the type ...
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Gene Complementation Question

Hi everyone! Here is a diagram of a genetics complementation problem. My main concern is regarding number 3d. I'm assuming that in this case, it would be complementary interaction and thus exhibiting ...
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What are some examples of genes that code for multiple proteins?

The title pretty much says it all. It is widely taught that a gene in a eukaryotic system could produce more than one protein due to post-transcriptional modification, but I do not believe I have come ...
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Telomere shortening during replication

It is widely know that each cell cycle during DNA replication some fraction of the telomeres is lost, and this phenomenon is called the end replication problem. Well this is due to the fact that the ...
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Pedigree Diagram help

I am asked to fill the genotypes in the spaces provided but looks like I am aving a little bit of trouble. can anyone help? thanks in advance!
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PedigreeAnalysis Genetics [duplicate]

Hello! I need help with this exercise question. I am not really sure which pedigree diagram is autosomal and which is not. But, is question b 1/2. Can someone give an explanation? Thanks very much in ...
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What is “transcribed strand”

This is an excerpt from a paper: T>C mutations at NpTpN trinucleotides, also found in hepatocellular carcinomas, shows strong transcriptional strand bias with more T>C mutations on the transcribed ...
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Process of Transcription

During the process of Conversion to Ribonucleoside Monophosphates the various ribonucleoside triphosphates break off their high energy bonds after linkage to the DNA.But the first ribonucleotide ...
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Regulation of chromatin structure

Recently, I reviewed the different levels of chromatin structure. The primary level is nucleosomes, where DNA is bound to histones, and has structural similarity to "beads on a string." The secondary ...
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What is the functional and structural distinction between core (H2A, H2B, H3,H4) and linker(H1/H5) histones?

Many explanations of histone biochemistry isn't quite elucidating for the undergraduate student. How does histone structure (dimers, octomers) relate to their specific functions as core or linker ...
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Histone marks mechanism

I am slightly confused about the mechanisms that makes histone modifications associate with gene expression. That is, H3K36me3 is believed to be present in actively transcribed genes, H3K27me3 in ...
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Transposons and the net amount of DNA

The retrotransposons and certain DNA-transposons, are "jumping" sequences which may be incorporated elsewhere in the genomic DNA of an organism, through varying mechanisms. This insertion is almost ...
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Regulation of the replication of mtDNA at embryonic level

While reading an article on mitochondrial inheritance I came across this link. The results state that mitochondrial DNA replication is regulated in different cells of an embryo at different levels. ...
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Ethidium bromide and mutagenesis on cloning

When performing a DNA cloning, sometimes PCR amplicon is run in agarose and it is detected by ethidium bromide marking under UV light. After that, gel is sliced, DNA extracted from gel....... until ...
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Which restriction enzyme would i use?

Plasmid pBr322 includes two genes that confer antibiotic resistance: a gene for ampicillin and a gene for tetracycline. The cutting site for the restriction enzyme BamH1 is in the middle pf the ...
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What is the reason behind choosing the reporter gene when experimenting on your gene of interest?

I noticed within example experiments in class that different reporter genes are chosen to be inserted near your gene of interest to prove whether or not the gene is being expressed. For example, you ...
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How does promoter sequence affect initiation?

I don't know if this might have been highlighted in recent research, but a textbook I have states that "the exact way in which promoter sequence affects [transcription] initiation is unclear" I'm ...
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Should the length of the electrodes in the electrophoresis chamber be proportional to chamber's size?

I am trying to build a small horizontal electrophoresis chamber from scratch. I want to use it for comet assay and I will be using only 1 slide, so it's going to be about 3cm wide, 10cm long and 4cm ...
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DNA and gene activation

As far as the genetic content of each cell is concerned I have read to my satisfaction that all cells of a person's body except the red blood cells (with no nucleus and so no genetic message) and the ...
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Transduction with P1 lysate prepared from strain that is proC::Tn10

If I do a transduction with a P1 lysate prepared from a strain that is pro*C*::Tn10 and the recipient is wild type, will all my recombinants be ProC- and Tet resistant since the Tn10 is in the proC ...
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Criteria for the numbering of human chromosomes

What were the criteria devised for the numbering convention employed in human chromosomes? When was it fixed? Correct me if I am wrong; it appears that chromosome pairs 1 to 22 were originally ...
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Can you detect if a mutation is spontaneous or induced?

Is it possible to determine if a certain specific mutation had a spontaneous origin (for example from a mistake of the DNA polymerase) as opposed to an induced origin (for example, from some genotoxic ...
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what is knob heterochromatin?

I am reading a paper which discusses Maize Genome Structure. Descriptions of the structure is given in the papers introduction. I know about heterochromatin "heterochromatin stains intensely, ...
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What exactly happens if during translation, an amino acid is not present?

Lets say that the cell wants to make a particular protein. Transcription of the appropriate gene is done and the mRNA is made. mRNA attaches to the ribosome and the translation is initiated in a "...
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Which part of the genome are the developmental sequences of embryogenesis located?

Which part or parts of the the genome are the sequences located. Are they spread across the chromosomes? If so how are they accessed sequentially with precision during embrygenesis?
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What tests can be performed to test the purity and quality of the raw peptide HCG (Human Chorionic Gonadotropin)

What tests could be run to test the purity and type of HCG? We are looking to purchase HCG from China but the purity and quality varies between labs, we are able to receive samples of the raw peptide ...
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When DNA is at its uncondensed form, what can it do?

I think it can do two things: The cell may be duplicating the genome during S phase. The cell may be transcribing the DNA into mRNA. Question: Can the two activities occur at the same time or one ...
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Smallest unit on which selection can act

Traditionally, the individual was considered to be the smallest unit on which Natural Selection (NS) acts. Today, we usually consider the gene as being the unit of NS. Of course, we should also ...
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Collective term for both exons and introns

Is there a term I can use to refer collectively to both exons and introns? By collectively, I don't mean ligated as with an unprocessed transcription product. I'm just writing about exons and introns ...
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Can Pfx polymerase add only one 3' A overhang?

I am trying to clone a PCR product that was amplified using Pfx polymerase into pGemT vector. I had to A-tail the PCR product using Taq polymerase since Pfx only generates blunt end products. My ...
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Is there a practical upper limit to amount of nucleotides or genes in a transformed plasmid?

I'm currently working on a synthetic biology project which involves working with lots of different parts. I would ultimately like to integrate these genes by transforming a single plasmid. I've heard (...
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Knockdown of long noncoding RNA (lncRNA) - how is it done?

I don't work at the wet lab and don't know all the details about the knockdown techniques. My question is: How lncRNA knockdown is done? For example - you have lncRNA that is functional in the nucleus....
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What is solid-phase bridge amplification?

During Illumina sequencing there is a step called bridge amplification by which DNA is amplified by isothermal enzymes. What is this stage, and how does it work?
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How do amino acids become attached to tRNA?

Is there a protein that catalyzes this or does it happen spontaneously? In which part of the cell does this happen?
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Gene & Protein nomenclature: N-Myc, c-Myc, et. al

Can someone explain (or point me to an explanation of) exactly what is meant by all the different symbols I see used for writing genes and proteins? I think I know that for genes, we use an italic ...
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Bicoid regulation of hunchback

I'm learning about development via the example of Drosophila embryogenesis. I understand that bicoid regulates hunchback, among other genes. My question whether the regulation is direct or indirect? ...
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Can DNA act as a translation substrate?

I get conflicting answers. One would think if it was true, it would be rather seminal and widely known. There are papers from Khorana[1], Holland[2], and Bretscher[3] (late 60s) that suggest that it ...
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PGC-1β Sod2 limiters/blockers

I'd like to block a percentage of PGC-1β or Sod2 expression. According to the following paper's figure beta-blockers inhibit some expression of PGC-1α. Are there any medicines/chemicals which safely ...
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mutant down but not out

I am interested in a gene which is null lethal but I need to temporary induce diminished capacity. If a cell is homozygous is it possible to induce heterozygous phenotypes or a partial knockout from ...
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methods for targetted deletion of genomic regions?

I would like to know what are currently used methods for targeted deletion of genomic regions in mammalian organisms or cell lines. I have heard of Zinc-Finger nucleases as a recent genetic ...
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Arabidopsis thaliana RCSB active site gene mutant

I'm looking for an Arabidopsis thaliana gene listed in RCSB with a clear mode of function and active site. In addition it needs to have an obvious phenotype when knocked out like severely retarded ...
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Why do DNA and RNA have the functions they have?

I know that there are two most important directions of genetic information transfer in living organisms: DNA->DNA and DNA->RNA. The first is replication, and the second is transcription. I wonder if ...
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How to clone and sequence a gene transcript of unknown sequence?

How might I go about amplifying a gene transcript (mRNA) from animal tissue of which little is known about the genome? In some applications, I have used reverse transcriptase PCR to amplify all mRNA ...
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How does the stem-loop cause intrinsic transcription termination?

In this animation, towards the end (about three quarters) the process of transcription termination is shown. It states that the transcribed RNA forms a hairpin loop (or stem-loop), which halts the ...
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How are DNA polymerase error rates measured?

It is well known that the first DNA polymerase, Taq, is quite error prone. Newer generation commercial enzymes that have either been isolated from different thermophile species or have been improved ...
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Vigorous shaking for HFR interrupted mating

I am trying to reproduce E. coli interrupted mating using an HFR strain, and I read that the cultures should be vigorously shaken at times to interrupt the DNA transfer from the F+(HFR) donors to the ...

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