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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How do the chemicals in our skin react with stainless steel?

What acid/chemical in human skin can react with stainless steel to leave a black mark on the skin? Why is it secreted/produced in larger quantities by some people and not by others?
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What sort of biofiltration is best for a small, portable, biofiltration unit?

I've been exploring the idea of a system to allow re-use (drinking) of RV greywater, or at least the freedom to dump in storm drains (I think the requirements are looser about this, but it still has ...
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How does zoo and laboratory animal feeding work?

What steps are taken to ensure those animals are fed adequately? When dealing with larger populations of animals, how is it ensured that all of those animals received food during a certain time period,...
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Why don't the heads of phospholipid bilayers repel hydrophobic molecules?

What I Think I Know: Hydrophilic and hydrophobic things repel each other. Since the cell membrane contains hydrophobic tails, it is difficult for hydrophilic molecules to pass through the cell ...
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Determining net charge of amino acid at given pH

I am trying to calculate the net charge on an amino acid, but I seem to be doing it wrong. The question I am trying to answer is "In a pH 7.0 buffer, what will be the charge of Methionine?" We are ...
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1answer
98 views

How long does it take for a blocked dopamine receptor to be broken down by the body?

Do the blocked dopamine receptors get broken down by the body and if so how often ? In other words how long does it take for the dopamine receptors blocked by irreversible dopamine antagonists to ...
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252 views

Chemistry of phosphodiester bond formation by DNA polymerase

As I'm teaching General Biology to my college students, I realized that I don't fully understand how a 3-P nucleotide like ATP is broken down to be incorporated into DNA during replication. How does ...
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1answer
8k views

Making sense of enzyme Km comparisons

I have encountered comparisons of the Michaelis-Menten constant ($K_m$) a few times. Generally speaking if the $K_m$ of an enzyme is higher, then its affinity to its substrate is lower. How does this ...
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1answer
87 views

What characteristic(s) of inverse agonists allow for inhibitory effects?

I know that inverse agonists have similar structure to its complement agonist; and, as a result, they have the ability to bind to the same receptor, causing an inhibition of the pathway considered. ...
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1answer
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Protein Pathways, Superfamilie, Function database/website?

I'm going trough some old data - but I'm running into this problem that all website we used use is not existing anymore. What I have is a very long list of proteins with accession number (refSeq from ...
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2answers
7k views

Difference between negative allosteric regulation and non-competitive inhibition

Both connect to some site other than the active site which controls the shape of the active site and causes the enzyme to be less active. So what is the difference?
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Is tyrosine hydrophobic or hydrophilic?

I’ve seen tyrosine classified as a hydrophobic amino acid due to its aromatic ring in some textbooks and as hydrophilic due to its hydroxyl group in other textbooks. How does tyrosine actually ...
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342 views

Enzyme kinetics at the chemical level

I am stumped by two questions: Why do we take only the initial 10%(or may be 9.99999....%) of S conversion as the rate of the enzyme reaction. why not more than 10%? Why doesn't the velocity keep on ...
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What happens at the top of the energy/enzyme graph?

At the very peak, the energy is in a state of activation energy. Here, is the substrate just attaching to the enzyme, or is is substrate already breaking?
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Why does pyruvate from lactate and pyruvate from other sources follow different pathways in gluconeogenesis?

My teacher taught me in a lecture that PEP forms from Pyruvate by two ways, based on their sources, that is - 1. If the Pyruvate was from lactate (by lactate dehydrogenase action), it gets shuttled ...
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1answer
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Arsenic (V) Reduction to Arsenic (III) by Microorganisms

I am currently doing research on arsenic toxicity in microorganisms, and I learned about arsenic (V)/(III) cycling. Arsenic (III) (usually in the form of arsenite) is generally 50 times more toxic to ...
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237 views

What is the advantage of using plant-derived antibacterials rather than bacteria-derived antibacterials?

So obviously we have a big problem with antibiotic resistance. Most of our antibiotics originate from bacteria themselves (or are synthetic variations on scaffolds which originate from bacteria). I ...
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84 views

How to characterize stability of a protein from Trp fluorescence vs [denaturant] curves?

A colleague of mine has taken Trp fluorescence measurements from a dimer in combination with various ligands, over a range of denaturant concentrations. The idea is that ligands which bind more ...
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Why isn't Fluorine, or Neon, the final electron acceptor in cellular respiration?

I'm a Chemistry student learning about periodic trends. I know that in (many organisms') cellular respiration, oxygen serves as the final electron acceptor due to its high electronegativity. However, ...
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How does garlic preparation affect its active compounds or medicinal properties? [closed]

I read the following claims about how to consume garlic: Consume immediately after crushing since the active compounds (allicin) is volatile and gets oxidized as soon as it's crushed Allow to sit 10 ...
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Can adenosine be cleared?

I've been thinking about this question for awhile, since reading this question: What causes adenosine build up in the brain when awake? We know that a couple of things will block adenosine receptors: ...
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1answer
67 views

Struggling to make sense of Km [closed]

So I have two substrates for one enzyme and I measured the product formation-> michaelis menten kinetics. The Vmax for both substrates is the same, the Km however is higher on substrate number 2. ...
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1answer
60 views

Glycolysis step 5: isomerization by triose phosphate isomerase

On the 5th step in glycolysis, triose-phosphate isomerase converts dihydroxy-acetone-phosphate to glyceraldehyde-3-phosphate. Now my question is: Why? Most books and sites I've read only say that ...
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1answer
242 views

How are Mono and Diglycerides metabolized without the Free Fatty Acids of Triglycerides?

Having difficulty figuring out what the body does with ingested mono and diglycerides if the usual process of TAG metabolism includes the FFA released from the TAG returning to the MAG to recreate a ...
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During starvation, does the human body do anything to prioritize which organs receive nutrients?

When food is scarce, the body slows its metabolic rate to conserve energy. Are there any other systems or processes that prioritize which organs receive nutrients?
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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. Am ...
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Could a mammal convert ingested dissolved CO2 to usable energy?

I'm trying to find out if it's possible that a mammal could orally ingest dissolved CO2 and convert it to energy for body heat, organ function, etc. Unfortunately, most of the scientific sources I've ...
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Which server to use for volume and accessible surface area calculation of proteins

I want to find the accessible surface area and the volume of a protein, giving PDB file as the input for the protein. I used two servers, 3vee and Vadar. For the PDB id, 1LTM, the websites are giving ...
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1answer
48 views

Why is free ribose not reduced to deoxyribose rather than the reduction occuring on ribonucleotides

I cannot understand why deoxyribonucleotides are not synthesized directly from deoxyribose, but ribonucleotides have to be synthesized first, and only then can deoxyribonucleotides be synthesized.
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Why is thymine not incorporated into mRNA?

I am aware that in transcription uracil bonds to adenine and not thymine. But what is it that actually prevents thymine from bonding to adenine in transcription, that is not present in replication?
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Does freezer burn affect only the cells on the surface of food?

Suppose i submerge a banana halfway through in a tray with water. Part of the banana is submerged in water, part of it is on the outside. The water and banana in the tray is being put in the freezer ...
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Are potential calories/ATP lost from fat when converted to ketones?

When insulin levels are low, the liver begins to oxidize fat. The liver oxidizes fat by an incomplete process that yields ketone bodies. The incomplete oxidation of fatty acids by the liver yields ...
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about lipid oxidation, does acid fatty transforms in glucose? [duplicate]

Lipid oxidation generates fatty acid and glycerol going into the bloodstream. Can they be converted into glucose by gluconeogenesis or are they turnd into ketone bodies?
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Is a fatty acid a polymer?

From my understanding, polymers are long chain molecules containing repeating units of monomers. For example, proteins are polymers called polypeptides with repeating units of (different) amino acids....
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Are unsaturated fats antioxidants?

Unsaturated fats contain double bonds like carotenoids (which is an antioxidant), and from my understanding, what makes carotenoid an antioxidant is that its double bonds allow it to undergo oxidation,...
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612 views

What biological processes can affect the temperature of the shadow a tree casts?

Assuming two trees have similar shape and leaf coverage, could differences in the biological processes among them lead to differences in the temperature of the shadow they cast? What biological ...
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Why does the oxygen produced in the photosynthesis come from water and not carbon dioxide?

In the photosynthesis equation: $$\ce{6CO2 + 6H2O ->[sunlight] C6H12O6 + 6O2}$$ The only place where we have 6 molecules of $\ce{O2}$ is in $\ce{6CO2}$. Then it reacts with $\ce{6H2O}$ to form $\...
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Where does the 'C' in exhaled CO₂ mostly come from?

When a human being exhales CO₂, what is, by the numbers, the main source of carbon atoms exiting the body in this way? I mean what class of cells, or which tissues are the biggest on a pie chart of ...
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Fruiting of trees — environmental stimuli and biochemical cascades

My question concerns fruiting of trees in general. However, I live in a tropical country (Philippines) where mango trees are ubiquitous, so I'll use it in stating my question. The question is about >...
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Why is funnel web spider venom so lethal to humans and not so much for other mammals?

According to the information from this article, People and other primates are exquisitely sensitive to funnel web venom but, intriguingly, other mammals such as mice, rabbits, guineapigs, dogs and ...
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1answer
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When forming an enzyme-substrate complex in a spontaneous reaction, why free energy increases?

We ate food, and then food was digested into proteins, carbohydrates... Does not digestion break bonds within food macromolecules? and thus free energy decreases? why when looking to the curve we see ...
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243 views

glycogenesis, glycogenolysis and weight gain or loss

I am under the impression (from dietary websites) that when excess serum glucose is stored as glycogen, body weight is increased and the reverse: when glycogen is converted to serum glucose, body ...
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4answers
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Where do the four ADPs come from in the second stage of glycolysis?

In the first stage of glycolysis, the two molecules of ATP are broken down into 2 ADPs + 2 Pi through hydrolysis, then in the second stage of glycolysis they are phosphorilazed to obtain 2 ATPs. How ...
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453 views

How do centrioles auto-locate to opposite sides of cell during mitosis?

I realize that centrioles are made of 9 triplets of microtubulin wound together with a hollow core, and that they are responsible for the configuration of the spindle during mitosis. The spindle ...
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Why does the ovum prefers to be arrested at metaphase 2 of meosis before fertilization? What is the possible advantage of this process?

Why does the human ovum prefers to be arrested at metaphase 2 of meosis before fertilization? What is the possible advantage of this process??Please help me with it.
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Light/Heavy Isotopes in Living Organisms

I was wondering, why are lighter isotopes (e.g. carbon-12 as opposed to carbon-13) preferentially used by life on Earth? Is their increased stability the only factor? Thanks in advance!
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Why does vitamin D need to be exogenous?

Vitamin D is a either a hormone or a precursor to hormones. It is very unlike any other vitamins, which are either cofactors or antioxidants, or may be other chemicals necessarily performing catalytic ...
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Can the excessive consumption of mineral water lead to kidney stones or other health issues?

I heard that drinking too much mineral (bottled) water could lead to problems such as kidney stones because of the high amount of minerals in it. Is it true? If so, what is considered to be excessive?
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Why are plants unable to take up Phosphorus directly in their organic form like Phytic Acid?

I am researching acquisition strategies of phosphorus by decidious trees. I am reading a lot that plants take up nutrients as their inorganic form. In the case of P according to literature this is ...
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How does low cysteine conditions affect pheomelanin production?

So we were studying this amino acid called cysteine. Specifically we were studying it's effect on melanin genesis. Our teacher told us how excess of cysteine affects the melanin synthesis by ...