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

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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 ...
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1answer
412 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 ...
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4answers
2k views

Why we have no enzyme to digest cellulose?

As we know, cellulose is the most abundant polysaccharide in nature. Why don't we have any enzyme to digest cellulose?
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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 ...
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2answers
369 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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1answer
187 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
200 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)?
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4answers
154 views

Are biological systems engineered? They are often reverse engineered at a molecular level!!

Understanding biological systems, molecular biologists need to “reverse engineer” them. Is this evidence that the systems were engineered to begin with?
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4answers
403 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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1answer
107 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 ?
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2answers
1k views

why is AUG the initiation codon?

Is there any reason why AUG is the initiation codon ? Why is there a need for an initiation codon ? Can't translation start with different codons?
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2answers
72 views

Assays during drug discovery

After researching the definition of Assay, I am left with the idea that an assay refers to scientific screening. It could be of chemicals, microbes, etc. I understand that during drug-discovery ...
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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
114 views

Suggestions for an experiment? [closed]

I would appreciate suggestions for my year-long AP Biology project. Such a project would consists of a standard experiment, to be done over the period of a year, so it would have >to be fairly ...
3
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1answer
692 views

What is DNA binding domain? It is not clear what the domain means

I am confused about the term DNA binding domain. Does it mean that there are some parts of the DNA that tends to coil up? Does it happen because some proteins tend to stick around that area? Also it ...
2
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1answer
44 views

Determination of gene direction

I have one sequence that composed of sequences of three genes. I should determine the direction of each gene, but two of these genes are disrupted, and I can't determine the initial codon. Does anyone ...
2
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2answers
165 views

Why did Fair Meiosis evolve?

How and why did Fair Meiosis evolve? I can hardly think that it provided a fitness advantage to the individual carrying the mutation. Why would it? Or did it evolve through lineage selection? Or was ...
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1answer
80 views

Randomness in living systems

The point of my question is not to talk about events that are uncontrolled by living organisms. My question is about controlled randomness, or I'd like to say adaptive random process. Process that are ...
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1answer
54 views

What method would you use to genotype SNPs in low quality samples?

What method would you use to genotype SNPs in low quality samples? I ideally want to genotype hundreds of SNPs in hundreds of scat samples (very low amount of target DNA, potentially degraded and ...
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2answers
60 views

The role of antibodies interacting with cancer

I'm learning about antibodies. As I understand it, antibodies detect stranger cells/bacterial/viruses by the molecules present in their membranes. In cancer cells, the cancer cell have produce some ...
3
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1answer
49 views

Self pairing in DNA

I know that ssRNA molecule can fold over itself (e.g. in t-RNA). Can DNA do the same? Is there any example of this in nature? Why is this phenomenon more common in RNA than in DNA?
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1answer
57 views

DNA preparation for sequencing

In shotgun sequencing method or some related method that DNA is break up into random fragment. The fragment that have about 3kb in size is inserted into plasmid by enzyme ligase and then plasmid ...
2
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1answer
54 views

How do cells figure out the big-picture shape?

I'm wondering what makes cells to divide (and stop) in such a way that they make our hands the shape that our hands are...
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 ...
3
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0answers
66 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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1answer
52 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
139 views

Why not use SDS-PAGE as a method to detect viruses?

Recently, I have been researching about DNA and I know the most popular method for detecting viruses is based on DNA. After learning about proteins, I wonder why we do not detect viruses based on ...
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2answers
99 views

Problem on finding sequence of Taq polymerase

As i know, Taq Polymerase can be found in Thermus aquaticus, so i do a search for protein list of Thermus aquaticus and have this : http://www.ncbi.nlm.nih.gov/genome/proteins/1724?project_id=55053 . ...
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1answer
104 views

Preparation of normal DNA polymerase

i don't need Taq polymerase. Just need normal DNA polymerase. So the main idea is preparation polymerase directly from Lactobacillus without using cloned vector. My idea is electrophoresis using ...
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2answers
108 views

Finding a easy and cheap method for dyeing dNTP

I want to measure OD to know the concentration of dNTP. Any idea for dyeing dNTP at cheapest price and easiest way ?
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2answers
300 views

Beginning with centrifuge experiment

This is the first time I do a centrifuge experiment with my own centrifuge machine, it's just simple made by a rotor that can rotate the tube at high speed. As I know a centrifuge machine can be using ...
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0answers
131 views

Can Pfx polymerase add only one 3' A overhang?

I am trying to clone a PCR product that was amplified using Pfx polymerase into pGemT vector. I had to A-tail the PCR product using Taq polymerase since Pfx only generates blunt end products. My ...
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1answer
86 views

Should I design a primer to detect virus based on NCBI genebank?

When I searched HIV on NCBI gene bank, I found 2 results from 1997: http://www.ncbi.nlm.nih.gov/genome/?term=HIV. HIV can change every day, so I think the sequence from 1997 is not useful. Is it?
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2answers
101 views

Realtime PCR plate cleaning

Have anyone used realtime PCR, is that the plate for realtime PCR is one-time using or not ? Otherwise how to clean the plate after reaction to prevent wrong result in next time using ?
3
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2answers
77 views

How does the DNA know which chain has error in repairing?

As we know, the DNA has more stability than RNA, if one chain has broken or accidentally distorted, it can be repaired by the other one. Suppose there is a segment AGTC, its peer is GACT. Now its ...
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38 views

Protocol for immobilize oligo to solid

I'm learning about microarrays and understand that an oligonucleotide can be immobilized to a solid like a CD acrylic plastic by modifying the oligo. Does anyone have a good protocol for modifying a ...
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1answer
54 views

Some question about materials for PCR

I'm planning to order oligo, polymerase, nucleotide, buffer for my first diy PCR experiment (now I have nothing), so I have some questions. How and how long I can storage them? I have only a fridge ...
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1answer
48 views

Carotenoid biosynthesis in yeast

Does Budding Yeast Sacchromyces cerevisiae produces significant amount of carotenoids? Have anybody estimated the ratio of flux going in branches 1. Cholesterol synthesis(via squalene) 2. Coenzyme Q6 ...
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2answers
187 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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0answers
40 views

Are stable proteins tagged by ubiquitin?

What would happen if an extremely stable protein was created because of some error? Would that protein be tagged by ubiquitin?
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3answers
126 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
117 views

Pump to separate protein/DNA instead of electrophoresis?

I know that DNA molecules or proteins can be separated in electrophoresis because the electrical charge is used to pull the DNA through the gel. So instead of using electrical, can I using physical ...
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1answer
694 views

What is the exact principle of capillary isotachophoresis?

I know it's a type of capillary electrophoresis, but I don't get how does the separation happen exactly.
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2answers
73 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
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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1answer
657 views

Why is allolactose the LacI inducer?

For what reason(s) is allolactose, instead of lactose, the "natural" inducer of lac operon repressor?
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1answer
465 views

How do viroids propagate to other hosts?

As viroids are simply non-encapsidated non-coding RNA molecules, it is difficult to imagine a mechanism for their continual infection, other than horizontal transfer which doesn't seem to be the case. ...
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0answers
640 views

Low RNA yield, low 260/230 ratio

I extracted total RNA from animal tissue using the Qiagen RNeasy kit, however my RNA yield was extremely low and the 260/230 ratio was around 0.3. This is the protocol I followed: The animal ...
7
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1answer
54 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 ...
2
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2answers
120 views

Prenatal Marketing

This is for a short story idea. Is it possible to modify the DNA of a child to make their metabolism more susceptible (physical response, addiction, etc) to a certain type of chemical i.e. a chemical ...