The study of the molecular processes of the nucleus and cell function.

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118 views

Shine-Dalgarno sequence and expressing proteins

Shine-Dalgarno sequence present in the prokaryotic mRNA plays a role in initiation of translation. In eukaryotes a Shine-Dalgarno like sequence is present but does not play an important role in ...
2
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2answers
56 views

Molecular simulations without capping n- and c-terminus of polypeptide

When running molecular simulations, what is the consequence of not capping the n- and c-terminus? I have been following gromacs tutorials and haven't come across any that deal with capping the ...
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2answers
179 views

How are antibodies designed?

Antibodies have the ability of recognising highly specific peptide sequences and bind it at their antigen-binding site. This ability is harnessed as a tool in research to purify target structures in ...
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1answer
57 views

Photosynthesis: Splitting Water

The splitting of water is an endergonic (non-spontaneous) reaction, and thus would require energy (chemical work to be done) in order to happen. In Photosystem II, an enzyme catalyzes this splitting, ...
2
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1answer
72 views

Determining sequence of oligoribonucleotide

Oligoribonucleotide X was treated with phosphatase (for removal of 3' and 5' - terminal phosphates), then with RNAase T1, which cleaves all phosphodiester bonds located in a 3' position of ...
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2answers
201 views

More variation in proteins than genes. Why?

The Genome of a cell or organism is the same as that of the entire organism. However, the proteome of an organism is much greater than that of each cell (unless the organism is unicellular). How do ...
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1answer
49 views

Clarification of the procedures to amplify cDNA needed

The typical procedure to obtain cDNA from genomic extracted DNA is the following: RNA is extracted from desired tissue, RNA/DNA hybrid is obtained by virtue of reverse transcriptase RNA dependent DNA ...
3
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2answers
74 views

Why not use Cu(OH)2 as a dye for protein electrophoresis?

As I know, $Cu(OH)_2$ $+$ Protein $\rightarrow$ Purple. So why not use $Cu(OH)_2$ as dye in protein electrophoresis?
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1answer
203 views

How much does the Hayflick limit/telomere length vary across taxa and within humans?

Since they seem to be quite connected, I'm curious if anyone knows of research comparing the Hayflick limit (and presumably by extension telomere length) between different taxa. I've heard the ...
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2answers
64 views

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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1answer
53 views

Isoprenoid Diphosphate Concentration in Yeast saccharomyces cerevisiae

Isoprenoid Diphosphate(IPP) is an important metabolites which is precursor in lot of secondary metabolites like Dolichol diphosphate, ubiquinone, prenylated proteins and carotenoid (not synthesized ...
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1answer
48 views

Protein Structure Statistics [closed]

Could you show me references of any works you know of where, 1- they take all the known protein structure data (that is the coordinate data of all the proteins in PDB database lets say or elsewhere) ...
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0answers
837 views

Bacterial 16S rRNA PCR amplification with universal primers

I am doing an experiment to amplify the 16S rRNA gene from bacteria present in gut contents of fish. After extracting DNA, I perform one-step PCR with universal bacterial primers (27F, 1492R) and I ...
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26 views

Where can I get yeast mutants?

I want to use some yeast mutants to conduct gene functional analysis, and the gene was isolated from plants. Can anybody give me some information regarding the websites or agencies from which I can ...
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1answer
66 views

Hypothetically, what is the smallest functional form of human?

Since the my first encounter with doraemon manga, I've been wondering many things, one of them is the small light. Assuming we had an instrument, such as small light, which enabled people to grow and ...
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2answers
299 views

Gel electrophoresis question

Leena is a molecular biology student. She purifies two fragments of DNA, 800 and 300 base pairs long. These were obtained from a plasmid after digesting it with HindIII. Each of these fragments has a ...
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2answers
1k views

Is wiping with RNAse Zap enough to destroy RNAse activity?

From the RNAseZap MSDS, it is an SDS at some unknown concentration, maybe with some NaOH? Some other links suggest there is some NaOH as well. The Ambion site states that RNAseZap destroys RNAse ...
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1answer
67 views

What will happen if we expose the brain to an intermittent light?

If a brain is exposed to an intermittent light are specific areas going to fire? If yes, which of them? Is there any experiment about this?
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2answers
96 views

Protein purification methods

Which of the following methods would yield the most purified protein fraction? A. Salt precipitation B. Charge separation C. Affinity purification The first one is the most commonly used, is it ...
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1answer
54 views

Electrophoretic mobility of isozymes

If isozymes are seperated using electrophoresis, which of the following will be the principle of separation ? A.charge density B.molecular weight C.polarity of molecule I think it should be B.
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1answer
45 views

Proportion of amino acids from a random polymer of U and C

A protein synthesis assay was carried out in vitro. A polyribonucleotide containing U and C in proportion 1:5 (positions of U and C are random) was used as a template. Which amino acids and in ...
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3answers
158 views

How to learn molecular biology through pubmed research articles?

Instead of using a textbook, is there an alternative curriculum, that simply lists a set of pubmed research articles for each topic covered in a typical undergrad molecular biology course? I am ...
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1answer
101 views

At what temperature does DNA re-anneal?

If primers weren't present in PCR at what temperature would DNA re-anneal? I am wondering how primers manage to bind on DNA strands before DNA manages to anneal back together.
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0answers
39 views

Shortest route for a Nitrogen atom from fossil fuel to a protein in your body?

Millions of years ago fossil fuels originated from plants. A nitrogen atom from fossil fuel is now inside in a protein molecule in your body. What is the shortest path that the nitrogen atom ...
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3answers
164 views

What does it mean for a distribution to be “consistent with a two rate-limiting stochastic steps”?

I'm reading a study (full text here) that examine the dynamic of nuclear translocation of a transcription factor in budding yeast, in response of calcium stress. They found that it occurs in bursts, ...
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1answer
661 views

How does blue white screening work in selecting E coli that have taken up a plasmid vector?

The plasmid vector I am referring to is pCR 2.1 - TOPO. I added the vector to the E coli and plated them up onto LB+amp+X-gal plate, then incubated. After incubation the plates had two types of ...
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2answers
323 views

Does bleach destroy RNAse activity, and if so, how does it do it?

I am working with RNA samples, and I'm trying to be very careful about RNAse contamination. I have some questions about bleach, though. Some people say that a solution of bleach is enough to destroy ...
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0answers
35 views

Adenosine metabolism

Are adenosine or its catabolites increased in inflamed airways? How can I assess this? I am trying to use inhibitors for adenosine deaminase, xanthine oxidase, and purine nucleoside phosphorylase, but ...
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3answers
962 views

How long can I store extracted RNA?

If I extract RNA from a (leaf tissue) sample using a one-step phenol:chloroform extraction, how long can those samples be stored at -80°C? And how many times can I defrost and refreeze them before ...
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2answers
84 views

Is there a Reverse Transcription optimization for long, 9kb, transcripts?

Has anyone optimized RT for long transcripts (9kb)? The downstream application will be PCR amplification and Illumina library prep. It will be trivial to make internal primers sets for the PCR that ...
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0answers
60 views

Large scale reverse transcription?

I need to make RNA:DNA duplexes. I can make 100 to 200 ug of mRNA through in vitro transcription, and I know how to use reverse transcription to make a cDNA library, but I have questions with this. ...
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4answers
424 views

Does RNA polymerase move around DNA or does DNA rotate benath the polymerase?

I'm thinking of the human genome specfically, but more general answers are welcome. As RNA polymerase moves along the DNA helix it follows a single strand. The two DNA strands are unwound locally ...
4
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1answer
151 views

Cloning two fluorescent proteins with different promoters in the same plasmid?

I want to clone two fluorescent proteins both driven by different promoters in a plasmid to be used to transform B. subtilis at the amyE locus. For this I want to use plasmid pSG1729 (Lewis and ...
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1answer
75 views

Do mitochondrial DNA have repair enzymes?

Mitochondria are considered endosymbionts originated from a prokaryote. So, do they have a DNA repair mechanism ?
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1answer
401 views

Why re-label the strand ends in 3' DNA labelling?

I have a problem with a molecular biology question; I don’t understand how DNA 3’ labelling works. I took a diagram from my lesson and tried to understand with it; this is what I understood. If I’m ...
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96 views

There are linear and rotary molecular motors in the cells. Do any of them have a fixed or stable frequency or speed?

Are there any linear, rotary or oscillatory molecular motors in the cells which can have fixed frequeny and which can be used as a reference for elapsed time timer? This question is with relevence to ...
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2answers
65 views

Termination of translation

What dissociates first - the last tRNA, mRNA and release factors or the subunits of ribosomes? I tried searching this from Lehninger but couldn't get a clean answer.
5
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1answer
127 views

Synthetic construct with multiple ORFs not expressing

I designed a synthetic construct on paper and got it synthesized from a company. The objective was to make a vector which can be used to study both transcriptional and post-transcriptional regulation ...
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0answers
36 views

Can DNA ploidy analysis differentiate field cancerization effects of oral potentially malignant disorders?

Can DNA ploidy analysis differentiate field cancerization effects of oral potentially malignant disorders [ Leukoplakia, erythroplakia, oral submucous fibrosis, etc] ?
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1answer
835 views

What is the purpose of Y-shaped adapters in Illumina sequencing?

Y adapters different sequences to be annealed to the 5' and 3' ends of each molecule in a library. The arms of the Y are unique, and the middle part, connected to the DNA fragment, is complementary. ...
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376 views

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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41 views

Why don't raisins lose water when in air?

It is common that we soak raisins in water, and they acquire water by endosmosis. That means that the cells are permeable to water, right? Then why don't they lose water when kept in air? Or kept in ...
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1answer
686 views

Molecular cause of cramps, spasms and strengthening in muscles? (incl. intro to muscle contraction)

When motor neurons are stimulated to trigger an action potential, this potential propagates down the spine, eventually reaching a neuromuscular junction, causing the release of acetylcholine (ACh). ...
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1answer
98 views

how to clone a gene fragment in two direction as sense and antisense in vector

I have a sequence ATG GGG CCC TTT AAA TAA and want to use it as antisense RNA in my vector. How should I clone it? I am confused with the direction of my clone. I looking for the direction and ...
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1answer
69 views

Complementarity of cDNA

Strictly speaking, what is the definition of cDNA? This confuses me, since usually it is said to refer to DNA that is complementary to mRNA. Is this correct? Is it restricted to mature mRNA? I ...
3
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1answer
431 views

How to secrete a recombinant protein from E. coli?

What are some secretory pathways that can be used to secrete a recombinant bacterial enzyme from E. coli? I have a recombinant protein (29kDa) that I will express in E. coli BL21 cells. For now I ...
0
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1answer
68 views

Why to choose a grammar from a lot of grammars that can describe structure of proteins? [closed]

Why do we choose a grammar from a lot of grammars that can describe structure of proteins? Usually, there are a lot of (maybe infinite) grammars that can describe one language. Why do we choose a ...
2
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1answer
108 views

How does GTP help in the step of codon recognition?

The anticodon of an incoming tRNA base pairs with the complementary mRNA codon in the A site.Hydrolysis of GTP increases the efficiency and accuracy of this step. How does GTP do so ?
2
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1answer
192 views

How to calculate or know by experiment the entropy of enzymes or protein?

How do you calculate or experimentally determine the entropy of enzymes or protein? In particular, I am interested in Boltzmann and conformational entropy, and Gibbs free energy. Any references are ...
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1answer
208 views

Can replication occur if DNA is methylated?

Can a methylated strand of DNA be replicated without removing methylation? Does it make any difference if the strand is methylated or not (during replication)?