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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2
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3answers
54 views

Choosing PCR conditions

How does one choose PCR conditions? Does it depend on the taxon, on the DNA concentration, on the primers or anything else?
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2answers
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Do all retroviruses evolve into dna viruses? [closed]

Since even nonprocreative sex transfers genetic material it seems redundant for viruses to destroy the host. Retroviruses are sufficiently simple to fit into DNA. So why not just become DNA viruses?
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1answer
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Is it Theoretically Possible to Create a Male clone from the donor Cell of a Female?

I understand that Dolly the Sheep was created without the presence of a sperm cell. Instead, nucleus DNA from somatic cells of adult sheep were used. Since Dolly was female, i am assuming that the ...
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2answers
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Are the DNA codon mappings arbitrary?

I am a Biology novice so I apologize in advance if I state anything incorrectly.... My question is, are the DNA codon mappings arbitrary? I understand that the DNA code is made up of codons which ...
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1answer
20 views

Is there a biological explanation for a 0.5 difference in allele size with PCR product?

CONTEXT I am currently working on a set of diversity, this diversity in interspecific (within the same genus). I am using SSR markers, the primers were designed on one species and are working really ...
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0answers
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Control for Bisulfite sequencing

I am wondering how can I control my converted DNA! I converted my DNA with bisulfite then I amplified the converted DNA with specific primers of BSP and purified my product and finally sequenced the ...
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1answer
29 views

Expected bands in polyacrylamide gel

I have something in my notes that doesn't seem right. If I use restriction enzymes on a PCR product how many bands should I see provided I know the restriction enzimes will cut the DNA? If I use two ...
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1answer
58 views

Antibiotic resistance

I have a biological puzzle that's been perplexing me for years. Can you review my logic and tell me where I'm wrong or if I'm on to something. As I understand it, most, if not all genetic ...
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1answer
43 views

What are the types of interactions in biological network (protein networks)?

In the KGML files, the types of relations between genes or proteins are precisely activation, inhibition, expression, repression, indirect effect, state change, binding/association, dissociation, ...
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1answer
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How do I reverse my insert within a plasmid?

I have a plasmid with: ...T7pro. -- RBS -- XBa1 cut site -- ProDpro. -- RBS -- AmilCP -- T -- Spe1 cut site -- T... How do I design primers to reverse the portion in bold, such that the T7 and ProD ...
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1answer
432 views

How does salt concentration affect chromatin compaction?

I've read that the primary obstacle to the compaction of chromatin is the negative charge on the DNA phosphate-sugar backbone. This negative charge is slightly stabilized by the positive charges on ...
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1answer
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Is ovum + ovum fertilization possible for human?

In humans is it possible to fertilize a ovum with another ovum from the same female subject? I already found some works in which the ovum is fertilized by a somatic cell (see e.g. this ), but I am ...
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3answers
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Is every protein encoded by just one gene?

Beadle and Tatum proposed the “one gene, one enzyme” hypothesis in the 1940s, and this was later modified to “one gene, one protein”, i.e. that one gene codes for one protein. Have any exceptions to ...
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2answers
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How were genes located before the development of bioinformatics?

I would like to know the detailed procedure of how scientists in earlier time were able to locate genes like how we were able to locate Huntington gene in 1983?
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1answer
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Why are not both alleles knocked out at the same time in knock out mouse?

I was reading this little 'article' about homologous recombination and knockout mouse. According to this article you first remove embryonic stem cells from a gray-fur blastocyst, then insert the ...
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1answer
116 views

What is the difference between alarmones and riboswitches

An Alarmone is an intracellular signal molecule that is produced due to harsh environmental factors. They regulate the gene expression at transcription level. A riboswitch is a regulatory segment of a ...
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998 views

What is the lowest common denominator of cancer?

What is the lowest level attribute that all cancers share? Also, what is the highest level attributes that all cancers share?
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1answer
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Do tRNAs that recognize multiple codons have any preference for one over another?

What are the effects of the different binding strength/affinity between the synonymous codons corresponding to a single tRNA ?
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What are the interactions between mtDNA and nucelus' DNA?

In an exam situation I have been presented with the following question by the teacher: What are the interactions between the mitochondrial DNA and the cell's nuclear DNA? To my knowledge there is ...
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1answer
61 views

How to attain a deep conceptual grasp of key atomic/molecular/genetic/ notions? [closed]

It's a total noob question, I know. I'm a layperson trying to come to grips with basic scientific terminology. I always face a conceptual hurdle in trying to understand micro-talk. The way I'm using ...
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What is the chemical mechanism by which PcP(c) is converted to PcP(Sc) in Fatal Familial Insomnia

I know the gene PRNP and it's location. There’s a mutation at codon 178 (asparagine found instead of normal aspartic acid) on the prion protein gene (also found in fCJD) and more uniquely there is a ...
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1answer
13k views

Difference between mutation and DNA damage

What is the strict difference between mutation and DNA damage? As far as I understand it, a mutation is an alteration in the genetic sequence, having "tricked" the repairing machinery and thus ...
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3answers
187 views

Have we ever observed fertile offspring with a different number of chromosomes than the parents?

Chimpanzees are supposedly the closest relative of humans from a DNA perspective, they are both diploid, and they both undergo meiosis. However, chimpanzees have 24 chromosome pairs while humans have ...
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1answer
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Reversal of cross-linking in ChIP-seq

Chromatin immunoprecipitation (ChIP) is a type of immunoprecipitation experimental technique used to investigate the interaction between proteins and DNA in the cell. A summary of the protocol for ...
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1answer
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Can I use commercial DNA loading dye for my RNA samples without degrading them?

I was wondering if I have to use special RNA loading dye or can I run RNA samples with regular loading dye that is used for DNA?
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1answer
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What hold and inject pressure to be used in microinjection?

I am planning to set up micro-injection apparatus in our lab. Normally what hold and inject pressures are used to inject DNA in fly embryo? I couldn't find in any literature as far as I've come across....
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1answer
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How are the very first telomeres added?

Here is an image of telomerase adding telomerase. As we can see, the telomerase sort of binds to a bit of the existing "3' flanking end of [the] telomere" - it's almost half and half. My question ...
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Gene terminology - is one gene a concrete, single physical sequence?

Suppose you have two identical copies of the same, coding nucleotide sequence (e.g. two copies of BCL2 - a random gene I found on Wikipedia). Could you say that these are two genes (i.e. the name "...
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Genetics… Translocation

Can a Translocation of chromosomal parts occur between an autosome and an allosome? If it occurs in between allosomes,what could be the effect of Robertsonian Translocation between an X and a Y ...
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1answer
284 views

Why does HIV chooses the Macrophage cells to infect first?

Upon entering our body HIV directs the macrophage cells to manufacture more virus particles. It injects the Viral RNA into the Macrophages. With the help of the enzyme reverse transcriptase the Viral ...
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Specific primer design

I'm designing primers for species-specific amplification (inside ITS1-ITS2 region). The problem is that when I blast (GenBank) my primer pair, the Forward primer anneals with some isolates (of the ...
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Do animals other than humans have different blood types?

Humans have the ABO and Rhesus blood typing systems. I have two questions about it: Why have we evolved these blood types? Do other animals have different blood types as well?
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Molecular genetics textbook (free?) suggestion for first time

I have never taken a molecular genetics course but want to prime myself for graduate school in the future. Does anyone have any suggestions or advice? A professor recommends "the molecular biology of ...
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1answer
2k views

How do DNA-binding proteins recognize 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-...
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1answer
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What determines the number of chromosomes an organism carries?

This is an extension of this question about What limits chromosomal length?. I am wondering what could be the specific reasons behind the number of chromosomes an organism carries. In other words, ...
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Differential Gene Expression

I have a matrix two gene expression datasets, one from 10 normal individuals and ten from diseased individuals, which are normalised log fold change values--, i.e., already processed. My question is:...
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1answer
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Are pheromones capable of activating changes to the Phenotype of a complex organism?

I know that pheromones are means of communication between the same species, but are they capable of changing the phenotype of an organism, may be influencing the expression of the genes of a said ...
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1answer
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Calculating number of amino acids in mRNA

Assuming there were 20 different amino acids and less than 40 types of different tRNAs found in this alien organism. How many amino acids would be found in the translational product of a 600-...
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1answer
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Gene density percentage

What do we mean when we say that: Haemophilus influenza genome is 85% genic. How do we measure gene density in percentage, especially for the above-mentioned case?
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1answer
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How to Calculate how many times an enzyme would cut a plasmid

I'm a little confused as to how to figure out the formula needed to figure this out. I have a plasmid that is 7.3Kb and am told that it is cut with an enzyme of 4bp. For some reason I thought that ...
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1answer
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Why is my DNA below the ladder?

I have run a gradient PCR.. and band 6 after the ladder is clearly the brightest. But all bands appear below the ladder. What does that mean? It is extracted mDNA that was loaded. Thank you in ...
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What determines the differences between differentiated cells?

Given two multi-cellular species with obviously different phenotypes. The reason for the different phenotypes reflects their different DNA. However two types of cells in an adult organism may have ...
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2answers
352 views

How does alternative splicing work?

I am trying to find out what controls what exons are spliced out, and I keep coming across the term cis regulator, but I cannot seem to find a clear explanation of what happens... Thank you in ...
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Why do eukaryotic organisms have introns in their DNA?

We touched on introns and exons in my bio class, but unfortunately we didn't really talk about why Eukaryotes have introns. It would seem they would have to have some purpose since prokaryotes do not ...
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2answers
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Is it possible to use virus for genetic modification of embryos during the fetus stage

I know this probably sounds rather hypothetical and not very feasible but I would very like an answer telling why it is possible or not possible and why. With the advancement of crispr and other dna ...
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2answers
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Why should you use an annealing temperature about 5°C below the Tm of your primers?

Why should you use an annealing temperature about 5°C below the Tm of your primers? According to my current research, I think it has something to do with the other reactents in the PCR, but I am not ...
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1answer
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Is female the default sex in humans?

I was taught in school that female is the default sex in humans based on the following logic: Development into a human male requires the activation of the SRY gene in the foetus. If that doesn't ...
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2answers
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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?
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1answer
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SNP vs common SNP

Wikipedia citing Nature defines SNP to be a one where each (thus the lowest frequency) allele exceeds some percentage threshold in the population. But I see a lot of papers and books calling such an ...
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What is the difference between average sperm epimutations and intersection sperm epimutations, in the context of the attached article?

The paper of interest is Manikkam et al. (2014). In research for a school Year 10 Science project, I came upon this article and the following two graphics. I don’t quite understand the difference ...