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

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The effect of the start codon GTG on translation in E. coli

Translation in E. coli is initiated at the start ATG codon, which encodes for the amino acid Methionine (Met). In some cases, the start codon can be GTG, which within the open reading frame (ORF) ...
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794 views

How do I prepare and clone from E. coli DNA?

I'm looking for a protocol to get genomic DNA from an E. coli sample so that I can clone a small portion of it using PCR into a plasmid. (< 500 bp in this case). It seems OWW (Open Wet Ware) ...
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946 views

Bacterial cell lysis - what solution to use?

I am trying to determine how quickly detergents act on bacterial cells (cell lysis). I would like to compare some detergents at difference concentrations for bacteriolytic activity. I don’t care about ...
7
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129 views

PDB Mining: Why Do I Find Atoms Less than 1 Angstrom Apart?

I am attempting to find potential Hydrogen bonds between Hydrogen donors and aromatic ring acceptors. I do this by predicting the location of Hydrogens on residues and then calculating how far these ...
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83 views

How to find miRNA binding sites on a specific gene?

I am trying to find miRNAs that bind to the 3'UTR of a specific gene. What is the best way of doing that (that is, with a good scoring analysis that is most commonly used by researchers in this area)? ...
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87 views

Selection on linked loci in a diploid population

Let’s consider two linked loci $A$ and $B$ that are both bi-allelic. In consequence, we have four different possible haplotypes $A_1B_1$, $A_1B_2$, $A_2B_1$, $A_2B_2$, which frequencies are $X_1$, ...
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414 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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57 views

Intracellular lipid transport

I know that lipids are carried around the body in the blood either as micelles or by lipid-binding proteins which allow them to be solved. Lipids can't always be integrated in a membrane though, the ...
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359 views

How fast do different organs turn over cells?

It is said that the human body turns over all cells or molecules in 7 year cycles. This is not quite correct, because there are different organs changing at different speeds. My interest is what is ...
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766 views

What is the mechanism of transgene integration (from expression vector to the host genome)?

How does a transgene (in vector) integrate to the host genome? (e.g. in glass bead method, neither biolistic nor agrobacterium). I already cut some parts (NdeI-PciI) of the vector (pUC18) and ...
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1k views

Difference in length of Okazaki fragments

The length of Okazaki fragments in the lagging strand is about 100-200 nucleotides in eukaryotes and about 1000-2000 nucleotides in prokaryotes. What (molecular mechanism, enzyme type ) ...
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46 views

circulating microRNAs are functional?

In plasma and other body fluids, miRNAs can be found. They not only originate from dying cells but also from active secretion and are usually 'packed' into vesicles/lipo-proteic structures (i.e. ...
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123 views

Does the MS2 RNA binding protein have any translational repression effects?

Reposted from Quora: http://www.quora.com/Does-the-MS2-RNA-binding-protein-have-any-translational-repression-effects I'm thinking of the MS2 protein binding to its RNA hairpin target. Would the ...
7
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163 views

What is the fastest way to build an alanine scanning library?

For interfacial studies, I would like to build an alanine scanning library for one of my proteins examining 20 sites. I will ultimately express the gene using E.coli cell-free protein synthesis. I ...
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4answers
1k views

What are good resources for self-learning modern molecular biology concepts? [closed]

My learning of molecular biology ended in the early 90's (and with early 90's era information). While I don't aspire to be a molecular biologist, I do aspire to better understand modern approaches ...
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298 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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2k views

Purpose of poly(A)+ RNA?

I am learning RNA-seq analysis. I always encounter this phase "poly(A)+ RNA". After searching, I got this: "Most messenger RNAs contain a poly(A) tail, while structural RNAs do not. Poly(A) selection ...
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751 views

Reverse transcription PCR optimization

What is the ideal amount of RNA to use for the RT? and how much cDNA to use then for the PCR? I did RT with a solution of RNA of 0.36 ug/ul. Then for my PCR I used 1 ul of the cDNA obtained and used ...
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109 views

DAM enzyme distances move along the genome

I am fusing a protein with a Dam enzyme (http://en.wikipedia.org/wiki/Dam_(methylase)). The idea is that when the protein binds to the DNA, the Dam enzyme will start methylating nearby GATC sites, ...
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269 views

How tolerant are ants to cold?

There was a trail of what are commonly known as sugar ants (small, brown, hyperactive) in my kitchen. Three of them walked onto an ice tray placed in their path. They only walked a short distance on ...
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4answers
509 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 ...
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2k views

What causes the colors we see in eyes?

Genetics aside, what are the biochemical reasons the different colours of human irises? Also, related, how does eye colour change, particularly in childhood? (example: my eyes used to be blue, ...
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234 views

Why does not the host produce any immune response to antiserum antibodies?

When an antiserum is injected to a person to protect oneself from a certain disease, the antibodies in the antiserum come from another organism. The question is: Why don't the injected antibodies ...
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18k views

What is the function of the RNA primer in DNA replication?

During DNA replication, RNA primase puts an RNA primer in the lagging strand. What is the function of this RNA primer? Why can't the enzymes put DNA fragments directly?
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213 views

What's the state of the art in designing and creating your own life forms?

What's the state of the art for solving the following problem. You imagine a set of features that you want a life-form to have. Just to take an arbitrary example, say you want your life-form to have ...
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255 views

Effect of histidine on the binding affinity of HisP

I was asked the following question by my teacher: A gene regulatory protein called HisP regulates the enzymes for histidine biosynthesis in the bacterium E. Coli. HisP is a protein whoes ...
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57 views

How exactly can dsRNA be introduced to a cell?

Is it just by viruses or are there other means by which it gets into cells, such as plasmid uptake?
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47 views

What regulates the timing of the motion of molecular machines during DNA Replication?

This question is about this video I found on Youtube. I just want to know what is the mechanism which regulates the timing of motion of the parts of these molecular machines. I know that those big ...
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1answer
363 views

How much does the distance between a transcription factor binding site and a promoter influence transcription?

Assume we have a synthetic construct with a minimal (inducible) promoter that requires activation for significant transcription to occur. Realistically, how important is the distance between an ...
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736 views

Does anyone have any TOPO directional cloning tips? [closed]

I'm just about to start working on a TOPO cloning after I couldn't get it to work with standard restriction/ligation. Does anyone have any tips for TOPO cloning?
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488 views

Why does replication require primers while transcription does not?

In transcription, there is no need for any primer. I guess the basic mechanism of DNA polymerase & RNA polymerase is the same. So why does replication have the need for a primer?
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2k views

Why is ATP the preferred choice for energy carriers?

Why is ATP the most prevalent form of chemical energy storage and utilization in most cells?
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215 views

In C. elegans, why does knock-down of cco-1 in some tissues increase lifespan, and knock-down of cco-1 in other tissues decrease lifespan?

Full question: In C. elegans, why does knock-down of cco-1 via RNA interference in specific tissues like body wall muscle decreases life span, whereas knock-down in the nervous system and intestine ...
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103 views

What are the lifetimes of cellular components on organelle or molecular level?

I was thinking that even though I know how generally the cell works, I don't really have a feeling of how volatile it is. I want to know what is the lifetime/turnover rate of different constituents of ...
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Very high 260/230 absorbance ratio of an RNA sample

After my most recent RNA extraction, the RNA samples had very high 260/230 absorbance ratios, (ranging from 5 to 25). I've never gotten numbers like this and I know the ratio is supposed to be ~2 in ...
6
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418 views

How does Topoisomerase II inhibition affect cancer cells?

Topoisomerase II poisons represent some of the most important and widely prescribed anticancer drugs currently in clinical use. These drugs encompass a diverse group of natural and synthetic ...
6
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1answer
109 views

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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409 views

How Do Adherent Cells In Culture Attach To A Plastic Dish?

I am particularly interested in MC3T3-E1 cells (mouse fibroblasts), which are adherent cells. Are hemidesmosomes involved in anchoring the cells to the plastic dish? What (if any) other molecules are ...
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1answer
80 views

Will eukaryotic RNA fold in the same way in prokaryotes?

As far as I know, there are no specific eukaryotic or prokaryotic factors that aid in RNA folding other than cellular environment (salt and ion concentrations, dissolved molecules, etc). Are there any ...
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295 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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547 views

How to avoid air bubbles while pipetting?

I get air bubbles while pipetting small volumes. How can I avoid them ?
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197 views

Can PCR tubes be made of different materials than plastic?

Does it matter if I replace the PCR tube (usually made of plastic) with another material like aluminum, glass, or something similar?
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99 views

What are the different ways an exon gets spliced?

Exons are produced by more than one mechanism, e.g. splicing out introns after transcription, if I remember correctly. Please list all mechanisms.
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66 views

Alternatives to trypsin for cell detachment?

I have ran out of trypsin and need to passage my cells (immortalized chondrocytes, C28/I2) today or tomorrow. I have been out of town and forgot to order more trypsin. I was wondering if there are ...
5
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425 views

What is the definition of a stringent/relaxed plasmid?

I have found a publication which proposes some definitions, including a definition for strict and relaxed replication. The definitions are: Relaxed control of plasmid replication. Relaxed control ...
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3answers
128 views

Finding a template/oligo combination for my first PCR experiment

I'm an information technology engineer. I love biology so I research biological topics and have an interest in PCR. That's why I have decided to create a PCR machine. Everything is done now and I ...
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3answers
3k views

What are the advantages and disadvantages of using beta-galactosidase compared to luciferase as a reporter gene?

In the University labs, we have used Beta-galactosidase as a reporter gene to quantify the expression initiated by the stress-response promoter in yeast. This was done by exposing one of the two ...
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2answers
3k views

Primer design for introduction of restriction sites flanking a gene of interest

I am wondering what the correct method for primer design to introduce restriction sites. Specifically between two methods. 1) Primer first partially hybridises to the gene, has a mis-match where the ...
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50 views

Protein Isolation from mammalian cells

What non-SDS buffer can I use to isolate protein from mammalian cells? The protein is intended for testing electron transport chain complexes.
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78 views

Hebbian theory “fire together” clarification

Donald Hebb states it as follows: "Let us assume that the persistence or repetition of a reverberatory activity (or "trace") tends to induce lasting cellular changes that add to its stability.… ...