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Questions tagged [molecular-biology]

The study of the molecular processes underlying life.

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69 views

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?
2
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1answer
61 views

What does “Origin” mean in NCBI GenBank?

I'm having trouble determining what exactly is meant by the term "Origin" in this case. It is just before a 70 bp sequence that the page claims is a plasmid, but does not specify it to be what I ...
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1answer
324 views

Why are prokaryotic promoter sequences written 5' to 3', when transcription proceeds from 3' to 5'?

It seems that the promoter regions are written from the 5' to 3' direction. My lecture notes, for example, give the -35 and -10 promoter regions sequences like so: Wikipedia seems to agree, on their ...
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1answer
79 views

How are single-stranded binding proteins removed from the lagging strand during DNA replication?

The lagging strand, downstream of the Okazaki fragment, is covered in single-stranded binding proteins (SSBPs) during DNA replication. What is the mechanism which ensures that SSBPs are removed from ...
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0answers
24 views

How to relate different phospholipid structures with entropy?

Phospholipids can form different stuructures like micelles, liposomes and bilayer. How can I relate this with entropy? ie explain different these different shapes based on entropy knowledge.
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0answers
58 views

I dont know what this means C16519T?

I was looking at a study done on SNP variation in mtDNA in people with HD, is this C-->T @ 16519 base position? I have no idea what I am doing so any help will do.
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0answers
80 views

How does gram-negative bacteria use high molecular weight starch if the membrane is only permeable to small molecular weights?

So one of my question is: The outer membrane of a gram negative bacterium contains pores that allow only molecules with a molecular weight less than 1,000 to cross. What does this bacterium need in ...
2
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1answer
44 views

Why is there a carbon atom without a greek letter in protein residues?

For protein residues I know that $C\alpha$ denotes the first carbon atom attached to a functional group. Each subsequent carbon is given a corresponding greek letter ($\beta, \gamma, \delta$) except ...
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1answer
20 views

Mice that have been reconstituted with geneX-transduced cells

I read this article in the following: ... Mice that have been reconstituted with geneX-transduced cells Now, someone who is not familiar with animal sciences, what does this exactly mean? ...
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0answers
33 views

How can I render a protein non-functional to avoid problem during expression?

We're expressing a protein in a model organism for crystallization, however it seems the protein has some toxic effect on the cells. Is there something we can do to make it non-functional during ...
4
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3answers
160 views

Knockout and knockdown of gene

Out of curiosity, I got this question whether knocking out (deletion) of a gene on one side and knocking down (RNAi) of the same gene on the other side will affect the cell in a similar manner or not. ...
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0answers
55 views

Assignment help: Transcription and translation

I was almost sure I had the right approach to this assignment until I got a variation of answer. Please help to evaluate my approach. An E. coli promoter has the following consensus sequence (Figure ...
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1answer
87 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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1answer
39 views

Building microtubules [closed]

I have some questions regarding building microtubules: Do alpha and beta monomers always exist as dimers when they are bonding to form tubulin? When tubulin structure is destroyed, do alpha and beta ...
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1answer
30 views

Help understanding cell replication animations

I often come across these animations about molecular biology showing for example how cell replication works, how virus infection works etc. Take this video as an example https://www.youtube.com/watch?...
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0answers
53 views

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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0answers
18 views

Will the addition of 3 amino acids in the C-terminal of a membrane protein affects its properties?

I am planning to use 2A self-cleavage peptide to express my gene of interest downstream of an intrinsic gene in my model organism so that I can exploit the intrinsic promoter, instead of cloning it ...
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0answers
11 views

transcriptional modulators

Transcriptional modulators are shown to be significant in differential activation/deactivation of genes, my question is considering recent advances in molecular biology have all the specific ...
2
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2answers
91 views

Are molecular machines encoded in the DNA?

I don't know much, if anything, about molecular biology. I watched the "inner life of the cell" on Youtube which triggered my curiosity about how these molecular machines came to be. My simple ...
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0answers
37 views

Sucrose inhibit onion root mitosis? Why?

I am doing an experiment about onion root growing. I had put an onion in different solutions of $C_{11} H_{22} O_1$ in H2O —with the root touching the water—: 0,1M; 0,2M; 0,3M; 0,4M; 0,5M. The ...
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1answer
40 views

How does gene affect organs development in eukaryotic cells? [closed]

I'm totally new to biology and apologies if you find this basic. The central dogma insists that genetic information flows in this direction: DNA -> RNA -> proteins So far so good, it is very clear ...
4
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1answer
2k views

What is the role of potassium acetate in plasmid extraction?

What is the role of potassium acetate in the alkaline lysis method of plasmid extraction? Earlier I was thinking its role is to shield plasmid DNA (the same as sodium acetate in genomic DNA ...
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0answers
36 views

Yeast transformation: is it necessary to remove template plasmid from PCR?

I'm frequently transforming budding yeast with PCR fragments. Normally, after PCR I digest with DpnI to remove the template plasmid. DpnI is a restriction enzyme which cuts methylated DNA, i.e. the ...
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1answer
74 views

Why replication collapse but not stall leads to DNA break?

I have been looking into the concept of replication dynamics and was wondering why collapsing but not stalling leads to a DNA break.
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1answer
74 views

Is there any evidence that supports glycolysis in mitochondria or chloroplasts?

Glycolysis is known to be a part of cellular metabolism undergone by both eukaryotic and prokaryotic cells, whether under aerobic or anaerobic conditions. As the endosymbiotic theory states that ...
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0answers
25 views

Quantification of concentration from chromatogram paper [closed]

In an experiment, I recently isolated and purified calf thymus DNA, hydrolyzed it with perchloric acid, and then applied the hydrolyzate to a Whatman paper in a polar solvent and let it run overnight. ...
2
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0answers
72 views

Would I expect salt precipitate on fibres of DNA in a NaCl water solution?

I just recently conducted an experiment in my biochemistry class where we had to add DNA to distilled water, isotonic saline and 2.5M NaCl. I noticed different physical aspects depending on the ...
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1answer
65 views

Blackgram leaves. SDS page. Phosphate buffer method

I am doing protein analysis in blackgram leaves by using phosphate buffer method. But I cannot get proper bands on my SDS-PAGE. What should I do to get proper bands?
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0answers
65 views

Proteins folds: relation to splicing and post-translational modification?

Is the secondary structure pattern of protein folds related in any way to alternative splicing and post-translational modification?
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0answers
739 views

Non-Competitive Inhibition vs Allosteric Inhibition

The Vmax of a reaction is lowered in presence of a non-competitive inhibitor (compared to the control - without a inhibitor) However, (Vmax of the reaction stays the same in presence of an allosteric ...
2
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1answer
30 views

Storage DNA Condition

It is possible to store a digestion of cells with lysis buffer several days at -20 degrees and then proceed with the phenol chloroform isoamyl purification? Thanks.
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1answer
214 views

Reading an amino acid physicochemical properties diagram

I want to know if I am reading the venn diagram correctly and why there are discrepancies in the diagrams. I'm trying to determine which amino acids are considered hydrophobic and I am using this ...
2
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3answers
99 views

What are the applications of predicting the structure of proteins?

Protein molecules are very important as they are used for catalyzing almost all the chemical reactions in the cell, regulation of gene activity and provide cellular structure. However, in predicting ...
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0answers
13 views

Adenosine receptor affinity states

Adenosine receptors have two different affinity states. Can an antagonist action like 1,3,7-Trimethylxanthine change the affinity state as a fast form of adaption, before new adenosine receptors are ...
2
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0answers
119 views

How is the effect of proof-reading on error frequency during DNA replication determined?

An article in Nature Scitable on DNA Replication and the causes of Mutation states that: When an incorrect nucleotide is added to the growing strand, replication is stalled by the fact that the ...
2
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1answer
844 views

What is the structural difference between beta and gamma globin chains of Hb?

Hemoglobins are tetramers composed of pairs of two different polypeptide subunits. The subunit composition of the principal hemoglobins are α2β2 (HbA; normal adult hemoglobin), α2γ2 (HbF; fetal ...
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1answer
78 views

Which cancers are routinely treated with anti-angiogenic therapy? [closed]

I have been asked to discuss 2 of these cancers and how the therapy is used. I understand angiogenesis and its role in tumour progression, but need some help in explaining how the therapy is used.
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1answer
74 views

Cutting of DNA strand [closed]

Would EcoRI cut the following sequence?? 😕 5'CTCGAGTTCGAG3' 3'GAGCTCAAGCTC5' What is the logic of cutting? Please explain how restriction enzymes work.
3
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2answers
65 views

Using evolutionary algorithms in molecular biology? [closed]

I am currently an MSc student studying molecular biology (on paper I'm a chemist) and soon I have to talk to my supervisor about my future, PhD research topic. Besides molecular biology I'm also ...
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0answers
84 views

The term when enzyme is “deformed”? [duplicate]

I am researching on the effect of hydrogen ions concentration (ph) on the rate of activity of enzymes. I currently understand that the hydrogen ion is charged and therefore would affect the ...
2
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1answer
57 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 ...
5
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1answer
211 views

What does the “Psi” in “Psi broth” stand for?

When making competent cells I've been using a medium called "Psi broth", which per liter consists of 20 g tryptone, 5 g yeast extract and 5 g MgSO4. Today I got curious about why it's called "psi". Is ...
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0answers
38 views

Are fMLP/C5a required for the respiratory burst to occur?

So in Janeway's Immunobiology 9th edition, it mentions about fMLP (fMet-Leu-Phe) as a chemotactic factor for phagocytes as well as also inducing a respiratory burst through downstream activation of ...
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1answer
65 views

Why is suicide inhibition considered a catalytic reaction when the catalyst is irreversibly modified because of the reaction? [closed]

I understand that this might be meaningless semantics, but I'm confused and would appreciate clarification. I've always been taught that, a catalyst is, by definition, a substance that is increases ...
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1answer
37 views

Using cell concentration [closed]

I am doing an experiment in which I plate for example 3x10^5 cells, and every day I have to count the cells growing. I find the number and a convert it in x10^5. In my graphs I have to use the cell ...
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0answers
19 views

Do all E. coli Express OmpC Membrane-Protein?

In a lot of papers I am reading, people are amplifying the OmpC gene (which codes for the OmpC membrane protein), from 'E. coli' but they do not specify the strain they used. According to my ...
-5
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1answer
54 views

Tumour cell injection into a mice [closed]

I am going to inject mice tumour cells into mice to create them tumours and I am wondering if I need to have special precautions for that, even they are cells from mice tumour I am afraid what can ...
0
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1answer
63 views

Reusing pipette tip

I'm new to research and one of the things I'm learning is pipetting. I've got the basics down but say I'm reusing a pipette tip because the solution I'm using is the same. So first I depress to the ...
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0answers
45 views

What is the point of storing biological samples in Trizol/TriSURE before RNA extraction?

The Wikipedia article on Trizol says that it helps break the cells and maintain RNA integrity during homogenisation of samples. Does anybody know by how much Trizol improves RNA integrity compared to ...
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0answers
8 views

Is the exchange of genes between bacteria also regulated by genes?

A lot of bacteria changes their genes by incorporating other genes given from other bacteria. But when a bacterium 'emits' a gene is this regulated also by a gene or is this proces done by other ...