The study of chemistry within the scope of biology: the compounds that occur and the reactions involving them in living organisms.

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Blocking buffer for actin and fetuin-b in western blot

I have been working on western blots for about a month now using actin and fetuin-b primary antibodies to no avail. My background is always high and I only had one good result. I want to know if there ...
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32 views

What is the source of the electrons generated in the Krebs cycle?

In the Krebs cycle where do the hydrogens and electrons that NAD+ and FAD accept come from? It seems that citric acid only loses two hydrogens because it starts out with six hydrogens and becomes ...
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53 views

Effect of pH on the hydrolysis of ATP

ATP hydrolizes to ADP and phosphate in a strongly exergonic reaction and is used for energy transfer and short-term storage in cells. ATP is stable inside a cell, so a significant activation energy ...
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38 views

Essential amino acids

Humans and the majority of animal species cannot synthesize essential amino acids (Info: Campbell biology 9th edition). However, meat, eggs, et cetera provide all required essential amino acids. And ...
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15 views

How do centrioles auto-locate to opposite sides of cell during mitosis?

I realize that centrioles are made of 9 triplets of microtubulin wound together with a hollow core, and that they are responsible for the configuration of the spindle during mitosis. The spindle ...
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1answer
14 views

Catalytic Triad of Serine Proteases

Is serine considered an acid in the catalytic triad involved in the mechanism of action of serine proteases? It is donating a proton to His but I am not sure if this really qualifies as an acid?
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44 views

Why is the protein ubiquitin so ubiquitous?

Ubiquitin is a protein tag that is attached to proteins in order to mark them for destruction/proteolysis by the cell. This system is sometimes used for clearing out harmful viral proteins that infect ...
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1answer
28 views

PBST vs. TBST buffer in western blotting

What is the advantages and disadvantages of using either PBST or TBST in western blotting, or while working with proteins in general? Are there other buffers which are also used for western blotting, ...
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44 views

Optimal pH of protein buffer? Basic principles to adjust buffers according method and analysis

Protein buffers such as PBST, which is used in western blotting, are normally adjusted to pH 7.4. When I try to find why, I find some information about optimal pKa for protein stability. Im not sure I ...
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29 views

How well can proteins discriminate between ATP and GTP? Can ATP act as a GTP mimetic?

GTP and ATP are similar structures with the adenosine and guanosine groups differing. Both are involved in a vast array of biological functions. However it has been shown that in certain cases, GTP ...
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37 views

Is there a difference in the energy produced from the hydrolysis of GTP and ATP?

Is the energy produced from the hydrolysis of GTP greater than/less than or the same. I know that GTP can be converted to ATP through a pathway and so my thinking was that GTP would be less.
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1answer
58 views

what do I need to use for protein protein interaction network

I would like to know what i should use to be able to build a PPI network. I have seen different structure for different techniques. for example sometimes the input look like this , each protein with ...
2
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1answer
77 views

What chemicals/substances exist in green capsicum (peppers) that do not exist in red capsicum?

I have known 3 people in my life that have incredibly adverse reactions (one called it an "allergy" and his symptoms did resemble such) to consuming any form of green pepper (capsicum) but have no ...
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28 views

Questions about Genetic algorithm paper of Gilman and Ross

I want to reproduce an (old) biochemistry paper of Gilman and Ross, i.e. " Genetic algorithm selecetion of a regulatory structure that directs flux in a simple metabolic model." ( The following link ...
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18 views

Looking for dataset of proteotypic and non-proteotypic peptide

I doing experimentation for peptide prediction using machine learning. I need some data for testing. My background is Computer Science. Any advice how to find proteotypic and non-proteotypic peptides....
3
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1answer
70 views

Forgot to vortex antibody before staining

Ugh. Did an immunofluorescence experiment last weekend, forgot to vortex both my primary and my secondary antibody solutions. And my final result looks dimmer than it should be. Is it possible that ...
4
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1answer
64 views

Why is the Pentose Phosphate Pathway so active in erythrocytes?

Is it because glyceraldehyde -3-phosphate (a molecule which when enter glycolysis help produce ATP through substrate level phosphorylation) can be prepared without losing an ATP through this process?
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1answer
42 views

Why does uncompetitive inhibition decrease the Michaelis constant?

I can't seem to find a good resource online that clearly outlines the difference between an uncompetitive, noncompetitive, and mixed inhibitor (I understand competitive inhibitor though). More ...
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2answers
127 views

Can the human body create glucose out of fat?

I read conflicting views about whether or not the human body can create glucose out of fat. Can it?
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1answer
22 views

Why is the formation of an enzyme-substrate complex endergonic (induced fit model)?

In the section about the induced fit model for enzyme substrate binding, my MCAT textbook claims that "The substrate has induced a change in the shape of the enzyme. This interaction requires energy, ...
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1answer
34 views

How does 2-mercaptoethanol lead to shift of the band to a higher molecular weight?

I have a project to isolate a protein with biological properties from a plant. The purified protein forms four bands with similar molecular weight on SDS-PAGE (30–35 kDa) in the presence of 5 % 2-...
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2answers
43 views

Do disaccharidases require a cofactor or coenzyme to function?

I'm doing research on lactose intolerance and am curious if disaccharidases (enzymes that break down disaccharides) require a cofactor or coenzyme to function? Reviews or references would be greatly ...
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1answer
60 views

Beta Sheets vs Alpha Helix - Strength

Is there a hard and fast rule of which one is stronger than the other, or does it depend on their context in a protein?
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2answers
60 views

Where do transamination and deamination take place?

The only information I know is about deamination is that it occurs in the liver and kidney. But in which part of the cell does deamination occur? To which tissues is transamination specific, and in ...
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1answer
42 views

Why does migration distance depend on log of molecular weight in SDS-PAGE?

I really want to know why in the result of SDS PAGE, log of molecular weight(MW) and migration distance (distance from the loading well) have a linear relationship. Why is it log(MW) instead of MW? ...
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1answer
30 views

Binding kinetics of 6xHis-Tag

For the planning of an experiment I would like to know the binding kinetics (kon and koff) of a 6x-His-tag to a Ni-NTA surface. I know they should differ due to surface quality and position of the ...
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31 views

Can the respiratory quotient be calculated from a formula or must it be measured directly?

I found the following question on the Respiratory quotient: A normal human diet has a Respiratory quotient (RQ) of approximately 0.85. Given that pure oxidation of fatty acids has a Respiratory ...
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80 views

Does the formation of water inside the mitochondrial matrix help contribute to the proton gradient during the electron transport chain?

Does the synthesis of water in the final step of the electron transport chain significantly increase the electrochemical gradient across the matrix? I understand that pumping protons out of the matrix ...
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9 views

What steps need to be taken between a successfull SDSPage GE and MS/MS?

Once you have your gel with separated proteins can you simple cut out each band and plop it into solution or do you need to take extra steps?
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286 views

What's the mechanism for being mentally tired?

I notice that after long tests, or long periods of critical thinking, my body and mind feel noticeably tired. Why does this happen? Are the neurons in my head not firing as quickly, or is there just a ...
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1answer
51 views

What is an interaction motif with respect to protein sumoylation?

While am reading about protein sumoylation this morning I got stuck on sumo interaction motifs and consensus motif line. I heard the the word motifs for the first time. What does motifs mean in this ...
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1answer
53 views

Use of western blotting

I ran across this paper recently. http://www.ncbi.nlm.nih.gov/pubmed/21151122 I am confused on their use of Western blotting. Their unmodified protein (no PTM group) has a band and their modified ...
2
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1answer
65 views

Electron balance for biomass synthesis: is my professor right?

I'm studying for my exam and I came across these notes written by the professor himself. He's talking about the general reaction of biomass production in a bioreactor: $$\ce{C6H12O6 + NH4+ + O2 -> ...
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2answers
50 views

Why is oxygen and CO2 measured in pressure instead of mmoles/L like other ions?

Na, K, Cl...All measured in mmol/L in plasma. Why is oxygen and CO2 measured in pressure (mmHg)? (I guess it has something to do with them being bound to RBC but I don't know why the difference).
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1answer
378 views

Why should phospholipid non-polar tails be “protected” in the membrane bilayer?

lipids are arranged within the membrane with polar head towards the outer side and non polar tails towards inner side, this ensures that the non polar tail is protected from aqueous environment. My ...
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1answer
20 views

How would one determine whether a chemical will upregulate a certain class of proteins?

I'm trying to determine whether certain organic chemicals will upregulate classes of proteins that possess deacylase activity.  How would I go about this experiment? I'm assuming I would use some ...
2
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1answer
104 views

How to retrieve logical expression (KO based) for reactions from KEGG?

Whether a module is complete or not can easily be checked by evaluating the Definition entry associated with the module; e.g. in module M00010, it is given by <...
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1answer
45 views

Lifetime of secondary messengers such as Calcium or IP3

Can anyone suggest me literature on the lifetime of secondary messengers such as calcium or IP3? A book would be preferred. What I am specifically looking for is a validation that secondary messengers ...
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22 views

Plasmid electrophoresis with DNases

DNases are used for treatment of cystic fibrosis. A normal DNase catalyzes the hydrolytic cleavage of phosphodiester bond in one strand of DNA. Scientists, in order to improve efficacy of DNases, use ...
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26 views

How do organoarsenics improve digestion efficiency in poultry?

It struck me as very surprising that these organoarsenic compound with structure looking not very compatible with living system is widely used as food additive to increase weight gain and improve food ...
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1answer
14 views

When is Pheophytin used in electron transfer to the q cycle in plants?

If I understand it correctly: (short version) The Q cycle starts with PQH2 it removes the 2H(+) and gives one electron to Plastocyanin and the other to a stored Plastoquinone to charge it to ...
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24 views

Insulin and leptin action on Anorexigenic Neurons in Hypothalamus?

Receptors for Insulin are present on liver, adipose tissue and muscles BUT also Insulin Receptors are present in arcuate nucleus of hypothalamus where it influences anorexogenic neurons through IRS2 ...
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1answer
38 views

Why are both glucagon and cortisol released in hypoglycemia?

Cortisol is released in response to prolonged stresses; one situation when cortisol is released is when blood glucose level is low. In this situation cortisol acts on adipose tissue promoting fatty ...
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Hyperglycemia in Type 1 Diabetes?

Glucose transporters GLUT1, GLUT2, are always present in hepatocytes membrane and GLUT3 on brain cells but the glucose transporters for skeletal muscles, cardiac cells and adipose tissue are not ...
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38 views

Fate of Acetyl CoA in well fed state?

When we have eaten well and take fat rich diet then in this condition Acetyl CoA produced from fatty acid breakdown will be gone to storage in adipose tissue or not? If it will go for storage then why ...
3
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25 views

Effect of ethanol and detergent on cell membranes problem

I am currently writing my biology report for an experiment I did on how ethanol and detergent affect the cell membrane. For my ethanol experiment, all went as expected BUT for my detergent experiment, ...
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1answer
65 views

Do two compatible tRNA codons bond together?

Can two tRNA with complementary anti-codons link together? For instance UUU with AAA. If not, why not?
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11 views

How were CDK1 and cyclin B identified?

I know that MPK is a dimer containing cyclin B and cdk1 and this promotes entry into mitosis. The experiment I have found was that when MPFs were micro-injected into frog oocytes arrested in G2, the ...
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28 views

Estimating RNA concentration from Specific Activity of Labeled RNA

The question reads, Using T7 RNA polymerase to transcribe in vitro a 100-nt RNA off a DNA template. This RNA contains 19 Adenosines. In your 100 uL transcription reaction you added 1.00 µL of α32P•[...
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How many ATP can be bound to f1 of ATP Synthase?

Diagrams show a bunch of ATP being produced simultaneously, is this possible? Or is it one ATP per rotation of ATP Synthase?