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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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3
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1answer
62 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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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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43 views

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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2answers
53 views

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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2answers
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Do histones constitute the largest proportion of the protein in chromosomes at mitosis?

Do histones contribute more (by mass) than non-histone proteins in the chromosomes formed during mitosis?
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2answers
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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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0answers
27 views

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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35 views

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 ...
5
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1answer
81 views

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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0answers
24 views

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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29 views

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
100 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
66 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
59 views

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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689 views

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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0answers
123 views

Living potato clock? [duplicate]

Could a potato stay alive and power a clock while growing in the ground? I know how a potato clock works as a electrochemical cell and involves chemistry, but I am only interested in a growing ...
2
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1answer
130 views

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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1answer
55 views

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
26 views

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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68 views

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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0answers
11 views

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
33 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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0answers
37 views

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
19 views

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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84 views

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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21 views

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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0answers
54 views

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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0answers
21 views

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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91 views

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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0answers
27 views

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
656 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
53 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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0answers
23 views

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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0answers
81 views

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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2answers
201 views

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? ...
8
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2answers
825 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
39 views

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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0answers
15 views

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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0answers
19 views

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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0answers
19 views

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 ...
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0answers
61 views

What is the fastest way to crystallise lysozyme (for student course)?

High school sudents are going to visit my university and I plan to demonstrate crystallisation of lysozyme. I ordered pure lysozyme from VWR. I can easily crystallise this within 15 min in batch (4% w/...
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1answer
414 views

Difference between prions and amyloid proteins?

Amyloid and prions are misfolded proteins, but what, if any, is the difference between them? Is amyloid a type of prion with a fibrillar structure?
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3answers
131 views

Is oxygen's paramagnetism biologically relevant?

It seems our most common everyday O2 molecule happens to be a paramagnetic one (see https://en.wikipedia.org/wiki/Oxygen). But, does this have a biological relevance as well? In other words, Do any ...
8
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1answer
226 views

Do chaperone proteins misfold?

If molecular chaperone proteins assist in the folding process of other proteins and misfolded proteins, can chaperone themselves misfold since they are also proteins? What would happen if chaperones ...
4
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1answer
37 views

How can sodium and potassium from burned organic matter (ashes) reenter the ecosystem?

If you thoroughly burn something you end up with bunch of oxides and hydroxides, as far as I know. Sodium and potassium hydroxides are plentiful in ashes, which is why lye was created by soaking ...
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1answer
22 views

Can someone help me interpret these charts on fluorescent polarization?

I have to present an article about binding designed proteins to fentanyl for my biochem class; I understand everything except how to interpret these charts on fluorescence at the very top of Figure 2a:...
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1answer
1k views

What is the importance of alkaline condition in biuret test?

Biuret test aims to quantify the amount of protein in a given unknown sample. Biuret agent contains copper sulphate, sodium potassium tartrate and Sodium hydroxide. Coppper ions form the complex of ...
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87 views

Chemical composition of human nucleoplasm?

I'm working on a computer visualisation of the inside of a human cell nucleus (embryonic stem cell for now if it makes a difference) and want a good approximation of the chemical composition of the ...
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1answer
48 views

How can P450 distinguish between foreign and native compounds?

It is my understanding that P450 enzymes are capable of selectively degrading compounds that enter the cell from the outside (e.g. synthetic drugs) without damaging compounds that are metabolic ...