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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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 ...
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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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2k views

Ripening bananas artificially: What is the biological reason

I am a resident of the tropical island of Sri Lanka, and we have a strange traditional method to ripen our banana harvest quickly. What we do is this: We dig a pit in earth that is enough to put the ...
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99 views

Ferredoxin synthesis pathways

I have been thinking about some alternative CO₂ fixation pathways. As almost all of them include ferredoxin reduction I started to wonder where does the ferredoxin comes from. I could not find any of ...
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49 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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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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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 ...
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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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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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2k views

Why is the DNA helix anti-parallel? [duplicate]

Why is it that DNA strands are running in anti-parallel fashion? Given the chemical base-pairing, they could have been parallel just as well.
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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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11 views

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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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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4answers
3k views

What implications has the missing 2'-OH on the capability of DNA to form 3D structures?

The chemical difference between RNA and DNA is the missing 2'-hydroxyl group in the nucleotides that build DNA. The major effect of that change that I know of is the higher stability of DNA compared ...
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31 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 ...
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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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64 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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24 views

Loooking for dataset of proteotypic and non-proteotypic peptide

I'm experimenting with peptide prediction using machine learning. I need some data for testing. I already have one dataset, but I need another one or two for verification. I'm looking for data for a ...
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2answers
367 views

What is the importance of urea in mass spectrometry?

What is the importance of urea in mass spectrometry? We use 8M urea to FASP our proteins prior to mass spectrometry. What is the significance of using 8M urea? and how does it affect the proteins?
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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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2answers
118 views

Light and Dark Reaction of photosynthesis?

I'm having a hard time understanding light and dark reactions because all the sites I've gone through provide different equations. Some say photolysis is H20 = H+ + O2 while some present it as H20 = H+...
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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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14 views

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?
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22 views

Does alpha-amylase from different species have different *optimal* conditions?

Do the optimal conditions for the enzyme isoforms differ between species? Specifically, do the optimal pH and temperature for alpha-amylase differ for that enzyme produced by B. lichiniformis and A. ...
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34 views

Amino acids in human cancer cells expose dextrorotation?

I would like to know if the amino acids in the human cancer cells are dextrorotatory or levorotatory. I mean the majority of them. They expose levorotation just like the amino acids in the normal ...
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3k views

Which are mobile and immobile elements in plants?

I am confused with this element or nutrient classification in the plants, since some authors set elements like $\ce{S}$ and $\ce{Ni}$ as mobile and other as immobile elements (Citation 1, 2, 3, 4, 5). ...
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286 views

Why is aconitase classified as a lyase?

Aconitase in the TCA (tricarboxylic acid) cycle isomerizes citric acid to isocitric acid via cis-aconitic acid intermediate. Since overall it functions as an isomerase, why it does not belong to ...
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33 views

Why are amides transported via xylem vessels? Why not phloem?

There is a statement in my textbook: "since amides contain more nitrogen than amino acids, they are transported to other parts of plants via xylem vessels" I wanted to know why the book ...
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30 views

Does CoA always bind to organic molecules through a thiol bond?

Does CoA always bind to organic molecules through a thiol bond? Sometimes I see it written as SCoA in textbooks but sometimes it's just written as CoA, are those actually chemically different, or just ...
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66 views

Do different emotions produce different tears?

Do tears of joy, laugh, grieve, and others contain different things or are they all the same?
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38 views

How many rounds of TCA Cycle would a complete oxidation of a triacyl(15-Carbon fatty acid)-glycerol, give?

This was a trickier question on a previous test, and I'm still not sure why, but the answer was "at least four". I answered "more than 22" and got it marked wrong. I assume that each fatty acid chain ...
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376 views

What is the transmembrane 'Positive-Inside Rule' nowadays? Has the definition changed over time?

First definition. Two publications by von Heijne in 1989 and 1992 coined the 'Positive-Inside rule' and showed it's practical value in topology prediction of transmembrane helices. It was clearly ...
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196 views

Are Gram negative bacteria classified as such because of their negative membrane potential?

Does the membrane potential usually quoted for Gram negative bacteria (e.g., E. coli) refer to the potential across both membranes? - If yes, then does the potential fall more over the inner or outer ...
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522 views

What is the difference between organelle membranes?

Cells and organelles are contained in lipid bilayers. I'm particularly interested in eukaryotic organelle bilayers and the biophysicochemical differences between them. Many papers assume a ...
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38 views

Can you replace glucose with glycerol in cell media?

In order to feed an animal cell in process called Respiration, can I replace Glucose with Glycerol? The Equation bellow: Glycerol + Oxygen -> Water + Carbon Oxide
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40 views

Link between NaCl and sulfide reducing bacteria

Could there be any link between the consumption of NaCl and sulfide-reducing bacteria? In my study on mice, sulfide-reducing bacteria (SRB) are more abundant, in high-salt-fed group compared to the ...
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529 views

Can excessive carbonated drink consumption lead to elevated red blood cell levels?

I've recently had a blood test and the results displayed elevated levels of erythrocytes as well as hemoglobin. (As a result my hematocrit levels were also above average) At my workplace there is a ...
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1answer
45 views

Diabetes Mellitus and renal failure?

I have studied that Diabetes Mellitus leads to kidney failure and that this is because of the damage to the blood vessels (especially the blood vessels in the kidney) due to high levels of blood ...
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1answer
34 views

Is there a difference between “Alpha Helix” and “Alpha subunit”?

In my biochemistry textbook the terms alpha helix and alpha subunit are both used. Are these two terms synonymous? For instance, hemoglobin has an alpha and beta subunit, are these the same thing as ...
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6k views

What is/are the molecular differences between HDL and LDL cholesterol?

Why exactly is HDL-cholesterol good for us and LDL-cholesterol bad for us. It has been well-established that LDL-cholesterol is associated with atherosclerosis and that HDL-cholesterol helps remove ...
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22 views

peritoneal dialysis Vs Hemodialysis?

Their are basically two types of dialysis: 1.peritoneal dialysis 2.hemodialysis, My Question is Why the peritoneal dialysis needs to be carried out on everyday BUT hemodialysis is carried out on only ...
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94 views

Is there nothing such as NADPH2? [duplicate]

I have gone through various sites and some say there is NADPH2 and some say there is no NADPH2 there's only NADP+ ...WHich is the correct view....Please dont mark this answer as duplicates since I ...
5
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70 views

How are ions 'pumped' across a membrane during electron transport?

A number of sites (including this one) that provide descriptions of photosynthesis state that high energy electrons 'pump' ions across a membrane. What is the actual 'pumping' mechanism? I've looked ...
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1answer
60 views

Which mammals cannot synthesize taurine?

It is fairly common knowledge that domesticated cats cannot synthesize the compound taurine. Other mammals seem to be able to synthesize taurine from cysteine [source]. Are there other mammals that ...
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2answers
103 views

What makes something food?

From my (limited) understanding, animals get energy from food by breaking chemical bonds between molecules. There's a lot of water here [citation needed], so it seems like natural selection would ...
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2answers
6k views

How does a plant grow before photosynthesis is possible?

During photosynthesis, a plant translates CO2, water and light into O2. I assume the carbon C is further used for the growing process. I wonder how the plant grows before the time where photosynthesis ...
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143 views

Does the use of RNA as a primer affect the accuracy of DNA replication in E.coli?

DNA polymerases have proof-reading ability, but RNA polymerase does not. Does the use of RNA as a primer affect the accuracy of DNA replication in E.coli? Explain
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29 views

Enzyme kinetics: recommended literature to grasp the concepts better

I have had a few biochemistry courses, but I still feel confused and a bit scared each time they try to explain and apply enzyme kinetics or even chemometrics in different situation during class. On ...