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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Apparant inconsistency in DNA topology theory in formation of origin of replication [duplicate]

I'm studying an introductory course in genetics and came across something I don't fully understand. I obviously used Google to find where I'm thinking wrong, but I still can't understand it. To ...
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Biochemistry conventions in writing the coding/noncoding strand

I am taking a biochemistry lab class, we work with plasmids, ligating protein DNA sequences to clone the DNA and then performing analysis on the protein (a beta lactamase) is most of what we do during ...
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Orientation of operator and promoter in E.coli expression vector plasmids

I am a biochem student and this has almost made me pull my hair out, here is the image of the question I got wrong, and I am not sure if the question is wrong or I am, I think the operator is ...
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How can SNP arrays be used to detect deletions within a gene?

I am reading a journal paper where the researchers are studying the effect of disease-causing mutations in the IL1RAPL1 gene. In the first figure of this paper, they show pedigrees of families where ...
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What is the difference between the positive/forward chain and negative/reverse chain of a chromosome?

I see these terms used to describe (what I assume to be) different strands, but I want to know, how is it decided which strand of a chromosome is the positive or the forward strand and which is the ...
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How to look for different transcripts for a protein?

I am trying to find all the different transcripts for a protein that translate into different isoforms of the protein. However, when I look it up online, there is no clear organized data on different ...
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What is the importance of radiation hybrid (RH) mapping in terms of genes?

I'm currently reading about radiation hybrid mapping with a TSP (traveling salesman problem) application in order to find an ordering of the genetic markers (i'm a mathematics student) and was ...
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Time required for DNA replication in E. coli

In a particular strain of E. coli, it was observed that DNA polymerase could add nucleotides to a growing chain of DNA at the rate of 600 per second. If the genome of this organism is 1.1mm long ...
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Why can SPRITE measure many simultaneous interactions?

Why is the SPRITE method not limited to a number of simultaneous interactions that can be measured, while microscopy and proximity ligation are limited to 2-3 interactions?
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Problem involving genetic interactions in yeast

I'm having difficulty with the following problem: In yeasts, genes MEC1 and SGS1 favor survival in response to HU (hydroxyurea). In the figure below, Δ indicates homozygosis for the mutant allele ...
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How many people need to have the same mutation of a gene in order for that gene to be seen as a feasible candidate for a disease?

I am learning about genome-wide association studies (GWAS) and I know that they are used to see whether certain SNPs are associated with a disease of interest. From everything that I have watched and ...
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How do geneticists determine if a gene mutation is pathogenic?

I am analysing information about patients with neurodevelopmental disorders using the DECIPHER genomics database. I am looking for patients who have only a specific gene deleted and no other mutations ...
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What does the 'y' mean in CHL1−/− / L1−/y double mutant mice?

I am reading a journal paper and I have come across the following statement: To investigate this, $CHL1^{−/−}$ / $L1^{−/y}$ double mutant mice were generated and analyzed for thalamocortical axon ...
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Recommendations for good books on bacterial genetics & molecular biology?

I'm starting a new phase of my PhD soon, and am feeling very under-prepared with respect to my general bacteriology knowledge. I was recommended to read up on basic bacterial genetics and molecular ...
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Why is the genetic code so heavily conserved?

Except some organisms, most organisms follow the same Genetic Code tRNAs, tRNA synthetases, ribosomes, etc. comprise the translational machinery for converting nucleotide codons to proteins. My ...
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3 answers
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Effects of mRNA vaccines on human body processes

I would like to understand the effect of an mRNA vaccine on more complex processes in the human body. To what extent does this "artificial", external addition of mRNA interfere with the body'...
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What is the difference between Haploinsufficient and Autosomal Dominant mutations

I have been reading a paper that classifies genes in different groups by the type of disease-causing mutations. The categories of mutations (alleles) it gives are: Haploinsufficient Autosomal ...
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Why does mitochondrial DNA have a high mutation rate, even though the mitochondrial function is highly conserved?

My understanding is that genes that are functionally important are more highly conserved. The DNA coding for ribosomal RNA is one example of that. I was surprised to find out that mitochondrial DNA ...
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What breaks hydrogen bonds while producing sticky ends using restriction endonucleases?

I am a high school student and I am little confused about the uses of restriction endonucleases. Why do hydrogen bonds(base pairing) break when restriction endonucleases produce sticky ends? If they ...
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1 answer
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How many MAOA alleles are there?

The question is about the human gene MAOA. I've seen MAOA-H and MAOA-L mentioned in papers. The page https://www.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000189221;r=X:43654907-43746824 ...
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homologous recombination and non-homologous recombination ratio during S-phase

Can I assume that it is easier to do targeted gene knock-in in rapidly dividing cells because they should have a short period of G1? Is there an easy way to measure the relative amounts of homologous ...
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Why do chromosome pairs have different shapes and sizes?

When I look at microscopic images of human chromosome pairs I see that they have different shapes and sizes. Is there a deeper biological reason for that? Is there some evolutionary pressure for them ...
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Why is BRCA-1 mutation a dominant mutation?

BRCA-1 gene is a tumor suppressor gene and undergoes a loss of function mutation to become cancer inducing. Why is it that only one allele needs to be mutated because loss of function mutations are ...
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What are the additional considerations for primer design in ancient DNA?

I'm familiar with the principles of primer design and have previously designed primers for use in modern DNA. However, in my current project I am working with ancient DNA (nuclear gene) and need to ...
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What's the process for determining whether a GC -> AT conversion in bisulfite sequencing is due to degradation?

I'm working on an ancient DNA project (humans) examining the methylation patterns for a single nuclear gene on chromosome 5. I understand the protocols of bisulfite sequencing, and in general how the ...
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Can chain-linked genetic segment data be used to reliably assign unknown relatives to either the donor's mother or father?

I am analyzing DNA matching segment data, and I am trying to broadly group all DNA matches by my donor's parents. Based on documented evidence, I can confidently identify "Person 'B'" as a ...
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1 answer
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What determines the nucleotides incorporated into RNA by polynucleotide phosphorylase?

Polynucleotide phosphorylase, in addition to its role as an exonuclease, is also involved in the post-transcriptional addition of nucleotides to RNA in a template-independent manner: “Polynucleotide ...
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1 answer
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Are there some natural instances of thermosensitizer?

Let's define thermosensitizer as any chemical or biological agent that can sensitize the cells to heat. In lab setting, thermosensitization seems to be achievable, such as by inhibiting chaperone ...
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Is 'constitutive effect' the proper term for explaining a biological effect that occurs due to the constitutive knockout of a gene in a mouse?

I am working on an experiment involving the analysis of expression of a protein X in wild-type (+/+) and knockout mice (-/-). In the knockout mice, the gene of interest has been constitutively knocked ...
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Does DNA have 5 nitrogenous bases?

Does DNA have 5 nitrogenous bases? I believe they are 5 because Uracil is not the same thing as Guanine, because, first of all, uracil "replaces" thymine, not guanine. And second, uracil ...
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Preventing the transcription bubble from occurring in an individual gene

I'm trying to find a way to stop the transcription bubble from occurring over a individual gene in humans. I need the act of transcription to be inhibited, siRNA knock down of the transcript does not ...
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What is the methodogy used to determine the exact genetic flow from one area to another and the times in which it flowed?

For example, I take the instance of Central Asian migration into India. Say geneticists studied a) ancient bones in CA b) ancient bones in India c) living people in Central Asia d) living people in ...
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Is P-Glycoprotein (or lack thereof) associated with sulfa drug sensitivity / allergy?

A deficiency in membrane P-Glycoprotein is known to cause toxic effects in some organ systems due to the increased bio-availability of drugs that are transported by P-Gp. Has it been shown that sulfa-...
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Will a Kozak sequence within a coding sequence interfere with eukaryotic expression?

I want to make a DNA vaccine for fish by using plasmid pcDNA3.1(+) with a bacterial antigen. Unfortunately, there is a Kozak sequence in the middle of my target gene. I am concerned that this Kozak ...
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How do we know genes that are considered endogenous retroviruses are actually endogenous retroviruses and not just ordinary genes?

What makes these genes different as to be classed as an endogenous retrovirus? I've read the entirity of Wikipedia on retroviruses and didn't find the answer. I think it could be that these genes are ...
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How does auxin-inducible degron technology make it possible to observe an immediate phenotype? [duplicate]

I am having trouble understanding this paper, which says Protein knockdown using the auxin-inducible degron (AID) technology is useful to study protein function in living cells because it induces ...
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What book teaches you about endogenous retroviruses [closed]

I'm interest in ERVs as evidence for evolution and want to learn more about them.
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What would an organism be like if its entire genome "worked"? [closed]

It is known that a large fraction of the genome of almost any organism "does not work", that is, it does not encode any proteins and does not participate in gene expression, in protein ...
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Is there any way to identify if chromosomes are inherited from the same parent?

I'm a PhD student in bioinformatics working on genomic data, and I was wondering: If I have access to a person's chromosomes, is there an assay that can determine that two chromosomes come from the ...
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Can Monsanto's (in)famous hybrid seed crops be cloned/grafted? If not, is there a technical or legal reason?

I understand that the seeds of a crop made from modern-day super hybrids will not, usually, produce the same quality plants in the next generation. Therefore, farmers have to buy new hybrid seeds each ...
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1 vote
2 answers
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Are SNPs or SSR copy number variation mutations more prominent?

I'm trying to get a sense of the dominant way that mutations occur. I have seen various numbers which seem at least at first glance to conflict, and I was curious if anyone had clarification on this. ...
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Genomic library preparation: Why does the restriction enzyme not cut into the gene?

I am currently trying to understand creating a genomic library more profoundly. In most textbooks I read (as well as wikipedia), they mentioned that the genomic library is created by isolating the DNA ...
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1 answer
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Is CRISPR being utilized when scientists use the CRISPR/Cas9 system to edit genes?

"CRISPR" and "Cas9" are different things. When a virus attacks a bacteria, the bacteria stores the viral code of the virus in CRISPR. And when the virus attacks again the Cas9 ...
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How was gene knock out done in pre CRISPR era?

I am trying to understand how CRISPR has made the gene knockout or gene editing process simpler to make transgenic animals. Here is an old (pre CRISPR) flowchart from Manis, 2007 that shows how ...
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How to identify the GPD gene when the sequence varies between organisms?

I'm reading a paper on genetic transformation of a fungi and the plasmid used in the paper uses two forms of the same GPD (glyceraldehyde3-phosphate dehydrogenase) promoter to drive a GFP gene, one ...
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Production of plant derivatives using genetic engineered micro-organisms

I saw a Thought Emporium video where spider silk was produced by genetically modifying yeast. I have also read about companies making vanillin (vanilla flavour) using this technique. I am curious to ...
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4 votes
1 answer
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Forward or Reverse Strand: Is there a difference when encoding genetic devices?

Background: In synthetic biology, and also in nature, there are lots of examples of genes in both the forward and reverse orientation. It seems in synthetic biology/bioengineering, most genetic ...
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Geometric Interpretations of the DNA Double Helix

In mathematics, a helix is a shape which has constant curvature and constant torque (see Wikipedia here. What are the biological implications of the DNA double helix having constant curvature and ...
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4 votes
1 answer
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What does z in lac z, y in lac y and a in lac a gene stand for?

In lac operon the 3 structural genes lacz, lacy and laca must have some reason behind their names. While lac refers to lactose but what does z, y and a refer to?
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4 votes
1 answer
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How can I change the payload of a bacteriophage used to transform E. coli?

I was looking at bacteriophages and how they're used to transform E.coli. While the whole process of how a bacteriophage works makes sense theoretically, I wanted to know how one goes about changing ...
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