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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What are these pathways called in Biology?

Considering the pentose phosphate pathway and the sulfate reduction pathway in bacteria; What are these types of reactions called in biology? Bio degradation reactions or bio transformation reactions ...
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6 views

What is isomeric threshold and isomeric count?

Found the terms isomeric point and isomeric threshold in the following paper: http://lib.gen.in/ocean/9064caa3202a71977f338ecb430280a7/10.1007%40s12539-012-0119-8.pdf It siad that the isomeric point ...
0
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1answer
22 views

Factors on which one compound transforming to another compound depend

Considering the Metabolic Pathway: http://www.genome.jp/kegg-bin/show_module?M00166 Consider the reaction R01523(the very first reaction). How is it possible to know that the compound ...
3
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1answer
18 views

How exactly is glyceraldehyde 3-Phosphate reverted to ribulose 1,5-bisphosphate for the continuation of the calvin cycle?

Around 6 molecules of G3P is produced at the end of the Calvin Cycle (light independent reactions of photosynthesis), and 5 of which are reverted back to RuBp. The general equation that I read is 5 ...
2
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1answer
20 views

What is the protein sequence taken as input in the Path-A prediction system

Considering the Path-A based metabolic pathway prediction (http://nar.oxfordjournals.org/content/34/suppl_2/W714.short). It uses machine learning for pathway prediction. Suppose that the input was a ...
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0answers
24 views

THYROGLOBULIN (19S) comes to a heavier position than ferritin (51S). Why?

Sedimentation values of thyroglobulin and ferritin containing iron are 19 and 51S, respectively. But, by density gradient centrifuge, it seems thyroglobulin(19S) migrates faster than ferritin(51S). ...
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59 views

Why do I smell chlorine when my sinuses are clogged? [closed]

I constantly smell chlorine after blowing my nose. I know it has to do with the sodium-chlorine ion channels but I don't know exactly what role they play. Related: I know in the disease "cystic ...
2
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0answers
47 views

What effects would be caused by exposure to common life forms with opposite enantiomer biology? [on hold]

Pretend a human had their body "reflected": heart on the wrong side, etc.; but also at the biochemical level: proteins, sugars, cells, DNA, everything. What would the effects be of that human's ...
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2answers
64 views

What is the difference between electrons and energy? [closed]

I'm studying microbiology right now and I have come across something confusing to me. I thought electrons provided energy to the cell by being incorporated into reducing powers and eventually driving ...
12
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1answer
142 views
+50

Solubility of DNA in water

This would seem to be an easy to answer question, but I was unable to find an answer (in g/L) for generic double-stranded DNA or plasmid neither on Google nor on BioNumbers. I would expect the ...
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0answers
68 views

With respect to kegg website [closed]

With respect to related R class in KEGG website: http://www.genome.jp/tools-bin/relclass?RC00064 What is the biological or statistical relevance of the score? How is it computed? And does it ...
2
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1answer
23 views

Question related to L-arginine biosynthesis

With respect to the L-arginine Biosynthesis pathway, the very first reaction converts L-glutamate to N-acetyl L-glutamate. In the linked reaction scheme, why are only L-glutamate and N-acetyl ...
2
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1answer
33 views

What does the Gini index mean in a biochemical context?

What is the meaning of the Gini index, as specificed in this link, which describes the Gini index of beta-glucopyranose bound to hexokinase? Is this true that if Gini index has a very low value that ...
4
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1answer
33 views

How does loss of the electrochemical gradient result in heat production?

As far as I understand, uncoupling of the flow of protons and ATP-synthase provides a bypass for protons between the outer and the inner membrane of mitochondria so that the protons don't have to go ...
5
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1answer
57 views

How does CO₂ concentration affect photosynthesis?

I have heard the theory that with the increase of CO2 in the air, the speed of the photosynthesis would increase, thereby limiting the increase of CO2 levels. What is currently the rate limiting ...
3
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1answer
65 views

Questions regarding a particular paper

With respect to the following paper: Automated identification of protein-ligand interaction features using Inductive Logic Programming: a hexose binding case study I have a few questions: in page ...
2
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0answers
15 views

Does blood typing still provide a use for ancient tissue analysis?

Modern techniques. In recent years, DNA sequencing has become extremely cheap. This, compounded by the ability to PCR miniscule samples to viable samples for analysis, means that aDNA can be ...
0
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1answer
33 views

What is the difference between polar and charged amino acids?

Chemically polar amino acids have an uneven (AKA polar) distribution of electrons over their surface. Charged amino acids have a charged ion in their structure. This is probably where my knowledge ...
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1answer
25 views

What is meant by clonal isolates?

With respect to this website: http://horfdb.dfci.harvard.edu/ what does the term clonal isolates mean?
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1answer
69 views

Why is the brain dependent on glucose?

The strict dependence of the (human) brain on glucose has always been puzzling to me. While ketones can substitute for a portion of the brain's energy needs, it cannot substitute completely: blood ...
1
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0answers
35 views

Importance of organic chemistry in biochemistry/molecular biology? [closed]

I'm halfway through my biochemistry and molecular biology degree in Australia and i'm concerned about a lack of organic chemistry. My friends studying biochemistry back home in Canada take units upon ...
5
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2answers
101 views

Proteins that give color (without fluorescence)

Is there proteins that have strong color, that could be seen without the need of UV and with naked eyes (with white light) - in mammalian cells? Searching for reporter, something like GFP, but that ...
4
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2answers
49 views

A doctor might give bicarbonate (HCO₃¯) to a patient who is breathing very rapidly. What is the doctor assuming about the patient’s blood chemistry?

The answer is: The doctor is assuming that the rapid breathing is the body’s response to low blood pH. (Source: Campbell Biology) But this answer doesn't make sense. Why would the doctor give the ...
2
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2answers
41 views

Recommend good conversational books to learn about cell and developmental biology or biochemisty?

I'm an engineer by training and teaching myself the basics of cell and developmental biology. I'm using Scott F. Gilbert's Developmental Biology and Alberts' Essential Cell Biology right now, and they ...
6
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2answers
87 views

The effect on the efficacy and potency of a non-competetive antagonist binding to the active site of the receptor (dose-response curve)

According to the book "Principles of Pharmacology: The Pathophysiologic Basis of Drug Therapy" by Golan et al, non-competetive antagonists can bind to both the allosteric site and the active site. I ...
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1answer
35 views

Why in acute phorpyria? [closed]

I am having confusing about treatment of phorpyria . I read it somewhere that for treating phopyria hemin and glucose is given IV . Please give me an easy explanation of it
3
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1answer
58 views

D/L configuration for amino acids

Why would this be "L-cysteine"? This is taken from the answer key for my biochem final. From what I understand if the -NH3(+) is on the left then the alpha-amino acid is in the L-configuration. ...
2
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1answer
37 views

Question regarding an Escherichia coli reaction

With respect to this link http://www.biocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=RXN-14479 Here the enzyme is mentioned and the two reacting compounds. Now , my question is 1. When these ...
7
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2answers
75 views

Is cyanocobalamin toxic?

I see that cyanocobalamin is not naturally occurring, and is synthesized in vivo to methylcobalamin. As part of the synthetic pathway, cyanide is broken off. All opinions I can find are that this ...
0
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0answers
21 views

Energy transformations in chemiosmosis and ATP synthase

In terms of energy, how does chemiosmosis drive ATP synthase? How does electrical energy turn into mechanical energy and then into chemical energy? Would the movement of $H^+$ be considered passive ...
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1answer
44 views

What is a new biotechnology issue? [closed]

I'm looking for any new biotechnology issue related to Biochemistry, Metabolic processes, molecular Genetics, or other relevant fields. If anyone knows of an issue that has solid resources around I'd ...
2
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1answer
22 views

Are more molecules of ADP than inorganic phosphate returned to the light reaction in photosynthesis?

During the dark reaction, 9 molecules of ATP are consumed for every 3 carbon dioxide molecules, yet only 6 molecules of inorganic phosphate ultimately leave the cycle. Does that mean that there is a ...
4
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1answer
64 views

When is Water Produced During Photosynthesis?

The formula for photosynthesis is: $$6CO_2+12H_2O \rightarrow C_6H_{12}O_6+6O_2+6H_2O$$ I can count the carbons, the waters on the reactant side, the oxygens, and the glucose, but I cannot seem to ...
3
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1answer
33 views

How Does NADPH Reduce 1,3-BPG?

If NADPH returns to being NADP+, then that means one proton and two electrons have been incorporated into 1,3-BPG. If only one proton and one electron were attached to the carbon in 1,3-BPG (removing ...
2
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1answer
20 views

Why are 2 electrons transported from photosystem II at the same time?

I only know that electrons are captured by the primary electron acceptor and then go through the electron transport chain, ultimately ending up at photosystem I. But why do 2 leave photosystem II in ...
3
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1answer
49 views

Why do some proteins “use” a beta barrel structure instead of alpha helices in transmembrane space?

Most proteins are fixed in the membrane by alpha helices. But some use beta barrels. Wikipedia describes beta barrels as used for porins, preprotein translocases, and lipocalins. To me, a coiled coil ...
4
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2answers
137 views

Do acetyl-CoA, acetyl-CoA carboxylase and acetyl-glutamate carry any charge?

Do the following compounds have any charge? If not, then why? If yes, is there any database that would give me this information if the compound is negatively or positively charged? The compounds are ...
5
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1answer
48 views

Do non-enzyme catalysed reaction pathways exist?

Can their be a kind of chemical reaction pathway in a cell, that is catalyzed or regulated but NOT necessarily by enzymes? I could not find anything on Google. I have almost no background in biology, ...
2
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1answer
34 views

What does it mean when a protein has a different excitation spectra than wildtype, but the same emission spectra?

We have a GFP mutant that displays a different excitation spectra with emission at 510nm than the WT. However, their emission profiles with excitation at 490nm are the same, and we do not observe the ...
3
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1answer
35 views

Applying kiwis on gelatin

Kiwis have the enzyme actinidain. This enzyme will break the peptide bonds from the gelatin. Making gelatin with raw kiwis will not work, because the peptide bonds in the gelatin will be broken down. ...
1
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1answer
32 views

What are the factors on which protein-protein interaction depend? [closed]

Does protein-protein interaction only happens when one of them is basic and the other acidic? Do protein interactions also depend on the protein structure? Are there more factors?
1
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1answer
28 views

Does creatine-phosphate (CP) supplementation regenerate NADH?

I have the following facts: It is possible to convert ATP <-> creatine vice-versa. (ref - non scientific) CP supplementation protects against metabolic syndrome. ref1 ref2 Fructose digestion ...
4
votes
2answers
50 views

Photolysis of Water?

In chemistry, I studied the decomposition of water as being $2H_2O_{(l)} \rightarrow 2H_{2(g)} + O_{2(g)}$. However, when water is split, the equation is $2H_2O_{(l)} \rightarrow 4H^+ + 4e^- ...
4
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1answer
53 views

Fats as energy source

As we know that the preferred source of energy for our body (source) are carbohydrates but heart muscle is an exception and need some explanation for this exception, that why the preferred source of ...
5
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0answers
46 views

SDS Laemmli Gel that did not solidify

In my lab class this week my partner and I were making a SDS-PAGE Laemmli Gel. We made the resolving gel solution which was made of 30% Acrylamide, DI water, 1.5 M Tris-HCL pH8.8, and 20% SDS. We ...
2
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1answer
146 views

Green Film Build up in Glass Water Bottle

So I have this Large Water Jug that I fill only water with. And this is the 2nd time there has been a layer of green film that builds up at the bottom of the bottle. I don't have any way of getting ...
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1answer
47 views

How is ATP involved in muscle contraction?

The sliding filament mechanism as explained by my text does not elaborate on how ATP is involved in the cross bridge binding and contraction process. How does muscle contraction utilize ATP? In my ...
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3answers
60 views

DIY storing family DNAs' samples for future uses (eg medical)

I have a question I could not get an understandable reply from Google and I am no expert in the matter, so my plead to you is if you could give me practical and relatively easy to follow advice. With ...
1
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1answer
43 views

Given an EC50 value, how do I reproduce the sigmoidal curve from which this was calculated?

All-trans retinoic acid (atRA) is a potent ligand for a nuclear receptor called retinoic acid receptor alpha (RARa). The concentration of atRA at which RARa is half maximal is 19nM. The dose-response ...
0
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1answer
32 views

ratio between heat transfer coefficient and thermal conductivity [closed]

Consider the Robin boundary condition for the diffusion/heat equation $\mathrm{u_t=a(t)u_{xx}+f(x,t)}$: $$\mathrm{-k(t)u_x(0,t)=h(t)u(0,t)}$$ or $$\mathrm{u_x(0,t)+\frac{h(t)}{k(t)}u(0,t)=0}$$ ...