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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57 views

How does the body “know” how to metabolize foreign substances

As a freshman biochemistry major, I find myself befuddled by our body's ability to perform complex chemical reactions to break down foreign substances. I can see how we would evolve explicit pathways ...
6
votes
1answer
466 views

How to Design an siRNA Experiment?

I'm going to undertake an siRNA experiment soon, but I have only read about them. I want to address the role an enzyme plays in processing a protein. From what I understand, I will need to pick two ...
6
votes
1answer
247 views

What's the difference between Ki and IC50?

I have just read this post at researchgate: "How to calculate experimental binding free energy from the IC50 value" I am not be very sure about what the difference is between Ki and IC50. Could ...
0
votes
1answer
29 views

Binding of Multivalent Antibody to mutiple epitopes?

A multivalent antibody molecule such as Immunoglobulin M Immunoglobulin A etc bind to more than one antigens or epitopes but I am confused about that wheather these multivalent antibodies bind to ...
1
vote
1answer
69 views

5,6-dihydrouracil and 5,6-dihydroxyuracil - how they arise in DNA?

5,6-dihydrouracil can be formed from cytosine after exposure of DNA to ionizing radiation under anoxic conditions [Ref]. What are other ways by which 5,6-dihydrouracil is formed in DNA? What about ...
4
votes
1answer
47 views

Do plants have preference for the form of nitrogen as nutrient?

In the nitrogen cycle (ecology), it is usually described that plants can use nitrogen in the form of ammonium (NH4+) and nitrate (NO3-). Do plants prefer one form of nitrogen over the other?
2
votes
1answer
25 views

Can plants directly use sulfuric acid?

In the explanation of the sulfur cycle, it is often said that sulfur moves from the atmosphere to the ground by acid rain in the form of sulfuric acid. Can plants directly use sulfuric acid to ...
7
votes
1answer
3k views

Why is fructose not glucose the main energy source of sperm?

The seminal fluid contains fructose as the main energy source for the sperm and not glucose. Why is fructose and not glucose the primary energy source for these sperm, since glucose is the ...
2
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0answers
33 views

Fatty Acid Synthesis of Fats Longs than 16 C

I understand that the human body when performing Fatty Acid Synthesis can synthesize only until C16 (palmitate). However the ER has desaturases and elongases. I know that desaturases are used to add ...
3
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0answers
79 views

Can cats use ketone bodies as only source of energy?

I recall reading that much of the energy a cat produces from its food comes from proteins which I assume would produce energy via being catabolised into amino acids which in turn, if glucogenic, would ...
59
votes
4answers
36k views

Why is uracil used in RNA rather than thymine?

What is the advantage gained by the substitution of thymine with uracil? I have read previously that it is due to thymine being "better protected" and therefore more suited to the storage role of ...
2
votes
3answers
60 views

Increasing/decreasing signal intensity in Western blotting

So I was in class and my professor was explaining western blotting. It seems as though there's more than one way to increase or decrease the signal intensity. He presented us the challenge to discover ...
2
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0answers
37 views

Glutamine analysis

I use to run a method to analyse all the amino-acids in a food sample. For that I have to hydrololyse the sample and in the last stage of the method I read the amino acids with a ion exchange ...
5
votes
1answer
57 views

Examples of genes involved in plastic responses

Adaptive plasticity involves sensing the environment and responding adaptively to it. Intuitively, I would think that this process may ask for a more or less complex genetic machinery of regulation of ...
2
votes
1answer
69 views

Domains in cell membrane

How is movement of proteins and lipids between different domains of cell membrane prevented? Why is the noncytosolic layer not able to do lateral movements between domains but cytosolic layer is able ...
1
vote
1answer
38 views

Clonidine's adrenonergic nature?

I am little confused here. I used the term adrenoagonist and sympatholytic to describe the compound. However, my teacher says that the correct term here is adrenomimetic -term. My understanding of ...
1
vote
1answer
25 views

To understand synthesis of e-NOS and n-NOS with respect to Ca and calmodulin

I found this sentence in my notes interesting E-NOS and n-NOS are Ca-calmodulin dependent ferments. They are synthesized in small concentration as a response to physiological signals which ...
2
votes
1answer
31 views

Does amylolysis occur in vegetables if stored below 0⁰ Celsius?

Assume that we have a plant, e.g. kale, which is prone to amylolysis if not harvested during a frost period. If it is harvested and put in a household freezer, such that it is frozen solid slowly ...
1
vote
1answer
41 views

Anesthetics, specifically inhaled anesthetics

I have had a look at previous inhaled anesthetics and many of them appear to be fluorocarbons. What could be the mechanism behind fluorine's anesthetic properties? Is it the specific bonding pattern ...
3
votes
1answer
64 views

PSI-BLAST website algorithm parameters

http://blast.ncbi.nlm.nih.gov/Blast.cgi In this website, when I want to apply the psi-blast algorithm on a sequence, under the section of algorithm parameters , what does PSI-BLAST threshold mean? ...
1
vote
1answer
506 views

Amino acid characteristics that determine their chemical properties?

What chemical aspect of amino acids results in their having different properties such that the chemical and physical properties of polypeptides vary with both amino acid content and amino acid order? ...
0
votes
1answer
57 views

What is the charge on oligonucleotide 5' pGpGpApCpT 3' at pH 7.00?

What is the charge on the nucleotide 5'pGpGpApCpT 3' @ pH 7.00? I thought adenine has 1 NH group and Guanine has NH and ...
-1
votes
1answer
50 views

To understand side-effects for nebivolol's beta1 selective pathway in PubChem? [closed]

Assume you have a drug nebivolol. When nebivolol is used as beta1 selective drug, beta2 is mostly for side effects, but this is not clear from PubChem. I do not know any cases where nebivolol is used ...
2
votes
1answer
47 views

How to manage fat-gluten oxidation in celiac disease?

Assume you have been in non-gluten diet 20 years. You built mass 8 mass with substances containing gluten (endogenous gluten stored in fat). Then, celiac disease is diagnosed. You have been 3 ...
0
votes
1answer
28 views

Can the same protein be represented by primary,secondary,tertiary structure? [closed]

As my book says: Protein can be represented by 4 structures. The primary structure represents the main chain and positions of amino acid residues. But actually, protein is not a rod but rather a ...
2
votes
1answer
41 views

Change in synthesis rate of a molecule changes equilibrium concentration

I was reading the topic of 'The concentration of the molecule can be adjusted quickly only if the lifetime of a molecule is short' from Molecular Biology of the Cell by Alberts. At the end of pg-837 ...
3
votes
1answer
65 views

What is the mechanism of action of lithium-induced polyuria?

I was reading in my pharmacology textbook on lithium in treating bipolar disorder, and I was curious to know if there was any specific action lithium takes to produce symptoms such as polyuria and ...
2
votes
1answer
28 views

What initiates primase to add an RNA primer to a DNA strand and what makes it stop?

What initiates primase to add an RNA primer to a DNA strand and what makes it stop adding RNA nucleotides? Is there tags added to the DNA back-bone?
0
votes
1answer
206 views

What is the exact chemical composition of human body? [duplicate]

I've just watched Breaking Bad Season 01 Episode 03. In that Walter gives the chemical composition of human body. The conversation is as follows Walter White: Let's break it down. Hydrogen. What ...
0
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0answers
18 views

To Study Interactions of two molecules in PubChem

Assume you have two substances Diosminum / Hesperidinum. The former strengthens vascular walls. The latter has role in some glycoside biosynthesis. From Biochemistry, I recall that glycodises have ...
6
votes
2answers
96 views

Can an organism process H₂O into H₂O₂?

In an answer to a recent question on Worldbuilding, I suggested that an organism convert $H_2O$ into $H_2O_2$. I suggested a few processes that yielded the desired final result ($2H_2O \rightarrow ...
0
votes
0answers
34 views

Substrate specificities of GPPS, FPPS and GGPPS (isoprenoid biosynthesis enzymes)

I have some questions related to isoprenoid synthesis enzymes. Does Geranylgeranyl pyrophosphate synthase (GGPPS) contribute in Geranyl-Pyrophosphate (GPP), Farnesyl pyrophosphate (FPP) and ...
4
votes
1answer
91 views

Identify the pink mold infecting refrigerated lemons [closed]

I made lemon juice 6 month ago. I just washed the lemon using brush and then cut them into pieces. Then I put one layer of lemon in the bottle followed by one layer of sugar Again one layer of lemon ...
1
vote
2answers
60 views

Are fatty acids and glycerol lipids?

As far as I know, lipids are defined as biomolecules which are hydrophobic. Triglycerides are composed of fatty acids and glycerol and are considered lipids but, are fatty acids alone or glycerol ...
3
votes
2answers
96 views

What are the physiological roles of Hydrogen sulfide?

I am thinking why hydrogen sulfide has its effects in the body. For instance, it is one Salmonella's virulence factor. I am not sure if such a balance equations holds H2O + H2S ←→ ... Actually, I ...
3
votes
1answer
78 views

Basic question about multiplex PCR

Let's say I have a DNA sequence with the following structure: $$ 5' - N_n - S_1 - N_{1000} - S_2 - N_{1000} - S_3 - N_n - 3' $$ Here, the $N$s represent stretches of arbitrary sequence of the ...
2
votes
2answers
302 views

Why would an Eadie-Hofstee Plot be non-linear? [closed]

Besides cooperativity between multiple active sites on an enzyme, what are the other reasons for the Eadie-Hofstee plot to be non-linear?
1
vote
2answers
550 views

Book Recommendations: GRE Subject Test In Biochemistry, Cell And Molecular Biology

There are probably a lot of really good answers that may vary significantly in terms of content. I'm looking for a set of books that I can read in preparation for the GRE Subject Test In ...
5
votes
1answer
87 views

enzymes that stabilize DNA loops

As a follow-up of a previous question, I would like to know what enzymes or protein complexes have been used to manipulate DNA samples into stabilizing DNA loops. I have read that cohesin is one of ...
24
votes
1answer
1k 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 bananas quickly. What we do is this: We dig a pit in earth that is enough to put the whole ...
1
vote
2answers
191 views

Is there a difference between polarity and hydrophobicity?

From literature the two terms seem to be interchangeable when discussing protein domains and motifs. But biochemically, what are the specific differences between these two terms? For example what is ...
5
votes
3answers
571 views

How does protein denaturation work?

I was wondering how protein denaturation works. Are there covalent bonds, such as disulfide bridges involved, or is it based purely on non-covalent bonds such as hydrogen bonds? Why is denaturation ...
3
votes
2answers
63 views

Tracking of oxygen molecules in glucose oxidation

For this reaction, found in typical biochemistry textbook: $C_6H_{12}O_6 + 6O_2 \to 6CO_2 + 6H_2O$ I am interested in where do the oxygen atoms of $6O_2$ go. I think they go to $6H_2O$, but this is ...
5
votes
1answer
88 views

Fermentation to acetic acid

How much time is needed for the fermentation to acetic acid production cycle, and the conversion of apple vinegar in a sealed container incubated at 37 °C? Should be in the fully closed? What is ...
4
votes
1answer
31 views

Phospholipid movement in cell membranes

What causes phospholipids to flow so quickly in cell membranes? In Biology by Cambell et al. they state that a phospholipids can travel up to 2 micrometers per second. Is that a random movement or has ...
5
votes
1answer
88 views

In which way would the yeast cell cope with the excess amount of methionine in the growth media?

I guess that when there is surplus of methionine in the cell it is incorporated in the TCA cycle as a succinyl CoA, with cysteine as a by-product. But now the cell has the surplus of cysteine. What ...
2
votes
1answer
862 views

What is the reaction mechanism of dopamine hydroxylase converting dopamine to norepinephrine?

The reaction is basically shown below. Dopamine hydroxylase is an enzyme, so I'm not sure if we can have a theory based on organic chemistry. On the other hand, maybe there is a theory that involves ...
14
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3answers
41k views

What is a coupled reaction and why do cells couple reactions?

I was wondering what exactly a coupled reaction is and why cells couple them. I read the wikipedia article as well as several others, such as life.illinois.edu but I still don't get it. Could ...
0
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1answer
163 views

Pathway mediates nitroglycerin-induced relief from angina pectoris [closed]

what kind of Pathway mediates nitroglycerin-induced relief from angina pectoris,please provide some idea...
49
votes
4answers
7k views

Why 22 amino acids instead of 64?

This question got me thinking about amino acids and the ambiguity in the genetic code. With 4 nucleotides in RNA and 3 per codon, there are 64 codons. However, these 64 codons only code for 22 ...