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Questions tagged [biochemistry]

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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Does cat urine really fluoresce? If so, why?

I temporarily got caught in the Sad and Useless website, and found Science is Fun. Most of the claims seem plausible, but I can't guess why cat urine would fluoresce.
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Could an uncut umbilical cord benifit a baby?

How long and would there be any benefit like adding an IV line to the uncut umbilical cord after a baby is born? Can keeping the umbilical cord attached (and for how long) be beneficial or harmful ...
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Can something cause both breaks and cross-links in DNA?

A double strand break in DNA is exactly that: the strands of DNA are severed. A cross-linkage occurs when something forms a covalent bond between two nucleotides in DNA. However, is it possible for ...
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SDS-PAGE compared to western blotting

SDS-PAGE and western blotting are both used to separate and isolate proteins. My question is, which technique should be used when? Does one of them has advantages over the other one?
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Fatty acid metabolism in children [on hold]

A 6-month-old infant is brought to your office because of frequent crying episodes, lethargy, and poor cating. These symptoms were especially noticeable after the child had had an car infection, at ...
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Cracking sounds made by glowing plankton

Recently I had opportunity to swim in place with glowing plankton, it was amazing experience and it as well gave birth to few questions in my head. I manged to google that they can glow thanks to ...
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what is ideal dose of peptide injection for mice? [closed]

What would be ideal concentration of 15 amino acidic antibacterial peptide and water (or buffer)? Injection rout is tail vein of mice and peptide is synthetic.
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1answer
149 views

How do organophosphates actually work?

The common explanation as to what the primary mechanism of action for organophosphates (and carbamates) is is the inhibition of the enzyme acetylcholinesterase and resulting buildup of acetylcholine ...
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1answer
57 views

Why magnesium ion is needed for activity of G-proteins?

I was studying about G-protein coupled signaling sysytem, somewhere they have mentioned about need of Mg$^{2+}$ for acticty of G-protein and related it to increase of cyclic AMP production. On further ...
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1answer
51 views

What is the difference among biochemistry, molecular biology, molecular genetics and structural biology?

I have never heard of straigthforward definitions of these fields in my college lectures, and the Internet searches were not very helpful. However, from what I have learned at different subjects, this ...
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1answer
45 views

Immunoprecipitation compared to western blotting

Immunoprecipitation and western blotting are both used to locate a specific protein within a sample and to isolate it. In immunoprecipitation, a specific antibody and agarose beads ( or other ...
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2answers
124 views

What structural features make a molecule a potent opioid receptor agonist?

For instance, take morphine. It is used as a baseline for measuring the potency of opioid agonists. Its structure looks like this: But then, take heroin, around three times as potent, its structure ...
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What substances can selectively destroy certain cells?

Recently, I've watched a documentary about how, in the 1980s, people were buying and using drugs from the streets and then becoming paralyzed a few days afterwards. The drugs that they were using were ...
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Preparing sample for SDS PAGE

I have more than 10 cell lysate samples (70 µL each) whose concentration varies from 1.9 mg/mL to 4.8 mg/mL. I have 5X and 2X SDS sample buffers. I would like to prepare SDS PAGE samples in such a way ...
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Is NMDA produced in the body?

On the wiki page for NMDA it says that NMDA is a synthetic substance that mimics glutamate. So why does the body not use glutamate instead of NMDA? Also how is it possible that our body can produce ...
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If fish gills do not split H2O into H2 and O, and just take the dissolved oxygen what is left leaving the gills? [duplicate]

Could you please explain to me the exact left overs after a fish takes oxygen out of H2O?
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Which Flocculant/Coagulant is ideal for harvesting Algae?

While dealing with Algae fit for human consumption (as protein supplements), which is the most suitable coagulant/Flocculant available? Factors to consider: 1) Cost Effectiveness (for instance poly ...
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What phosphorylates tau protein & and what causes tau to be phosphorylated?

I want to know what phosphorylates tau protein and its 6 isoforms. I know kinases cause phosphorylation events, and in tau it can be phosphorylated in a healthy neuron in the trans conformation, but ...
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1answer
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Backbone hydrogen bonds between adjacent amino acids in a protein?

Is it possible for two adjacent amino acids in a peptide to form hydrogen bonds between the backbone NH and CO? Are there any examples of such situations in proteins and how common are they? If ...
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which enzyme phosphorylates sodium potassium pump?

I know that Na+/k+ pump possess atp-ase function; so the pump will hydrolyze ATP into ADP + Pi. And I see in a figure that the pump is phosphorylated but couldn't really find which protein catalyzes ...
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Intein Splicing

Currently I am trying to read and understand this paper on intein splicing. https://sci-hub.tw/https://www.ncbi.nlm.nih.gov/pubmed/22001202 However, I'm a little confused with Figure 4. Why do the ...
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1answer
52 views

Does digestion require hydrochloric acid?

Would our digestion function any differently if we secreted something else, like sulfuric or nitric acid, instead? I'd assume an acidic environment may be required, but not sure if chloride is also ...
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1answer
46 views

If overcooked hard boiled eggs show these green sulfide rings, why do scrambled/fried eggs not show this?

In the image above, the dark green rings are ferrous sulfide rings, caused when the sulfur from the egg white reacts with the iron in the egg yolk when the egg is overcooked. I was wondering, given ...
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1answer
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Is it possible to stop more/extra fat from being stored in the body?

I don't mean simply by restricting eating or upping the activities, but a way to basically stop the body from adding more fat on itself down on the bio level. For example, I'm not too knowledgeable on ...
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Do cats produce DMT?

Edit: If somebody (anybody) wants to add an answer so the bounty won't go to waste, please do so! The comments have already introduced me to the Kegg metabolism database, some interesting papers, and ...
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1answer
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Does every protein starts with Methionine amino acid [duplicate]

During process of protein synthesis we need AUG Codon to start translation .As we know this codon codes for Methionine amino acid so can we say that every protein starts with Methionine amino acid ?
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What are the (evolutionary) advantages of secondary transport?

Secondary active transport uses electrochemical gradients as a source of energy for the uphill transport of substrates (coupled to downhill transport of the ion). However except for in a few cases (e....
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1answer
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Exocytosis of synaptic vesicles

I'm reading the following paper: http://jcs.biologists.org/content/123/6/819 The part I am really confused about is when they say: Exocytosis appears to use two alternative pathways: clathrin-...
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What is the difference between Warburg effect and Crabtree effect in metabolism? [closed]

In addition to answering my question, please suggest a good review article that provides comparison of the above effects. Which pathways affect central carbon metabolism to produce these effects? Also,...
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Rhodamine 123 Staining Function

How does Rhodamine 123 act as a probe for Mitochondrial Staining? What is the Exact Biochemical Basis? and can it Stain Chloroplast as well? Thanks in Advance
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2answers
29 views

Base pair and amino acid weights? [closed]

How does a base pair weigh approx. 650 Da (which is two paired nucleotides) but an amino acid (3 nucleotides) weighs only approx. 110 Da ?
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Can sperm cells penetrate the cell membrane of non-ovum cells?

Sperm cells have tiny bags of enzymes on their tip (the acrosome) which allow them to penetrate the ovum. My question is whether or not the process that allows sperm cells to penetrate the cell ...
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1answer
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Lysosomal Storage Disease

In my biochemistry class today we did a problem detailing two lysosomal storage diseases. In the first scenario, a cell line for I-cell disease can synthesize lysosomal hydrolases that are perfectly ...
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The truth behind human urine and marking territory?

So some years ago, I remember watching a survival show in which the host said that human males produce a type of chemical in the urine that animals such as wolves can acknowledge as a territory marker....
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The effect of salt, pH and temperature to the salivary amylase

If I prepare the following set of tests, incubate for 15 mins, then add 2-3 drops of iodine solution to each test tube: Salt test (1ml starch solution + 0.5 ml enzyme + 1ml 1M NaCl, incubate at 37 oC ...
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Can the heart and other muscles function without creatine/phosphocreatine?

Skeletal muscles in the body have a small reserve of ATP. During the first few seconds after contraction, phosphocreatine is used by the enzyme creatine kinase in order to phosphorylate ADP to ATP ...
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How is it possible for phosphate to form two ester bonds in DNA replication?

I understand that in phosphodiester bond formation, two hydroxl groups on the phosphate molecule bind to the 3' and 5' OH groups on two independent pentose sugars. This is a condensation reaction, so ...
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Is there a relationship between HDL-C and LDL-C?

For a gentle introduction to cholesterol and its functions, see a great answer on SE Biology Whenever I read about how to deal with cholesterol level, the rule is to keep a low LDL fraction, ad a ...
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Where do the protons in the mitochondrial intermembrane space originally come from?

I'm currently reviewing this concept in cellular respiration. The book which I'm using is Reece, Minorsky, Campbell's Biology and while it does a good job at explaining the process involved in the ...
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How to recreate bioluminescence in a lab?

I have several mg/mL of D-luciferin, luciferase (firefly), ATP solution (25 mmol) and MgSO4 (for the mg2+ ions). The experiment has to be done in cuvettes of 2,5 mL (if I get any results, it will be ...
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1answer
46 views

Does eating nonsalty food with MSG make you thirsty?

Assume that you're thirsty after eating food that didn't taste salty while you were eating it. Quora posts and https://msgdish.com/msg-problems-and-answers/ still impute the thirst to salt: The ...
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1answer
45 views

Depolarisation of post synaptic neuron

When the post synaptic neuron begins to depolarise as positive sodium ions move into it and it reaches threshold- does the inside of the neuron actually switch to being more positive than the outside? ...
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Valence electrons in DNA nucleotide addition [closed]

Can anyone explain the movement of valence electrons during the nucleophilic attack that occurs during DNA synthesis? The 3' oxygen starts with two lone pairs of electrons but what happens during the ...
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Does our brain use up more ATP after smoking cannabis?

kind of an amateur here. If the firing of the neurons' signals uses up some ATP, and smoking cannabis makes them fire off more quickly, do our brains use up more ATP to sustain that rapid firing?
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Is the chemical composition of urine detrimental or beneficial for a tree?

Seeing as a lot of people around the world urinate against trees it came to mind that I never thought about how the tree responds to this. Is it detrimental for a tree if people urinate against them? ...
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692 views

Where does the proton come in the reduction of NAD?

In our curriculum biology textbook the reduction of NAD+ is depicted as follows: NAD+ + 2 H+ → NADH + H+ If this proton in the products was not present in the reactants, then where does it come ...
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1answer
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Where do the lysines come from during ubiquitination?

I know that Ub forms an isopeptide bond with lysine, but where do the lysine come from? Are they just always available for the Ub to find to during the ubiquitination process? Is there a free lysine ...
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What proteins are assisted by chaperone folding?

I've been looking into a lot of papers, and most say that chaperones assisted in the folding of misfolded proteins, or Ubiquitin markers aggregates for degradation by the proteasome. Or it will say ...
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Cadmium Poisoning and Toxicity Mechanisms

Is anyone aware of the toxic mechanisms of specific instances in which cadmium ions can interfere with cellular functions resulting in acute cadmium poisoning?
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Toxic Metals and Oxidative Phosphorylation

I was reviewing the toxicity of certain toxic metals, specifically cadmium and their effect on Oxidative Phosphorylation and Cellular Respiration, I have found that metals such as cadmium inhibit ...