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Questions tagged [thermodynamics]

Thermodynamics in biology is the study of energy transfer within and between cells, organisms, and their environment, including the underlying chemical reactions.

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Sweating at all temperatures

Is sweating possible if surrounding temperature is below the body temperature? How the sweating occur due to the combustion of food?
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Calculating fraction of protein unfolded from spectroscopy data

This is a question from a homework pset of previous year. We are given the absorbance at 222nm of both a wild type and mutant protein at different temperatures. We are then asked to calculate various ...
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Despite the highly negative free energy change in ATP hydrolysis, why does ATP not spontaneously undergo hydrolysis?

the delta G0 of hydrolysis for two terminal phosphate group is around 7.3Kcal/mol, so why does ATP not breakdown spontaneously? Is it because it has high activation energy?
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How are cell death like apoptosis and entropy related?

In Perspectives on Statistical Thermodynamics, Yoshitsugu Oono, it is written that Do not conclude, however, that since the second law is invincible, information thermodynamics is unimportant. It ...
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Computing equilibrium constants of unsymmetrical reactions

I'm looking for the equilibrium constants of unsymmetrical biochemical reactions from the database, Thermodynamics of enzyme-catalyzed reactions. For instance, enzyme 4.1.2.13 catalyzes the ...
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How to relate different phospholipid structures with entropy?

Phospholipids can form different stuructures like micelles, liposomes and bilayer. How can I relate this with entropy? ie explain different these different shapes based on entropy knowledge.
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Why is the separation of biochemical synthesis pathways safer and more economical?

During our first lecture of plant physiology, our teacher told us that the separation of biochemical synthesis pathways was advantageous because it was safer and more economical. The problem I got, ...
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What does enzymatic equilibrium in % represent?

I am studying an enzyme which can catalyse a chemical reaction in both directions. The paper I am looking at is mentioning a thermodynamic equilibrium of 1% in the synthase direction. What does that ...
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If you are 30 degrees, and touch something that is 50 degrees, do you only feel 20?

First off, I don't know if this is the correct site to post this question as it could possibly fit into others? If so, please flag it to be moved as I would appreciate that very much. Now, if my body ...
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How can dehydrogenation steps in some biochemical pathways produce ATP?

Dehydrogenation reaction of alkanes are inherently endothermic as one removes two thermodynamically more stable C-H bonds and replaces it with one less stable C=C. Although the product is conjugated ...
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Entropy increase or decrease in an reaction

My question is how would you tell if the product of an reaction has more or less entropy than the reactants? For example, in glycolysis, when glyceraldehyde-3-phosphate becomes 1-3 ...
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The second law of thermodynamics and the cell (3 questions)? [closed]

How is that the cell maintains internal order, yet it discharges heat (disorder) to the surrounding? If the cell is supplied with materials for metabolism and growth by the surroundings (disorderly ...
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Energy transfer from P680 to oxygen-evolving complex

This topic is confusing me. As I understand it, in the PS2, photons are used to split water into molecular oxygen + protons and electrons in the oxygen-evolving complex. To do this, a photon is used ...
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How fast can the human body temperature change?

I'm really curious about how fast can a human body temperature change? E.g. how fast can the human body temperature change when the human has fever? I'm not interested in how fast fever changes the ...
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Can enzymes catalyze thermodynamically unfavorable reactions?

Can biological enzymes catalyze thermodynamically unfavorable reactions? I read that an enzyme lowers the activation energy of a reaction by offering an alternative reaction pathway with a lower ...
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What characteristics of the protein folding process ensure that the energy landscape is a funnel?

The folding funnel hypothesis states that the energy landscape that proteins observe when they fold is funnel shaped with a single global optima. This ensures that no matter what sequence of folds the ...
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Difference in ATP synthesis in mitochondria and chloroplast

The mechanism of ATP synthesis in mitochondria and chloroplasts are almost the same, but there is a big difference: the f1 particle in mitochondria uses 2 H+ ions to synthesize one ATP, whereas in ...
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Redox potentials in photosynthesis light dependent stage

In my lecture notes, it states ...there is a significant thermodynamic problem due to the respective redox potentials of the half reactions: H2O<--> 1/2 O2 + 2H+ +2e- pE=+0.82V ...
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Gibbs free energy and its change for the hydrolysis of ATP

So in my book I have the reaction $$ATP \rightarrow ADP +P_i$$ and hence $$\Delta G^0 = G^0_{ADP} + G^0_{P_i} - G^0_{ATP}$$ This is easily understood, but I have not been given any actual ...
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Thermodynamics of spontaneous protein folding: role of enthalpy changes

I'm trying to get clear why protein folding occurs spontaneously. $$\ce\Delta G=\Delta H-T\Delta S$$ According to thermodynamics the ΔG should be negative for a process to occur spontaneously. When ...
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Do the pH and other ions affect the hydrolysis of ATP

ATP hydrolizes to ADP and phosphate in a strongly exergonic reaction and is used for energy transfer and short-term storage in cells. ATP is stable inside a cell, so a significant activation energy ...
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What were the camels' humps good for back in the polar areas?

I've heard that camels lived in the North America formerly and just in the last few thousands years they've migrated to the hot deserts. Thus they allegedly utilized the adaptations against the cold ...
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Why don't membrane proteins move?

I understand that based on their tertiary structure, intrinsic proteins have hydrophobic non-polar R-groups on their surface and that they 'interact with the hydrophobic core of the cell membrane to ...
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Why is statistical mechanics relevant to RNA and protein folding?

This is a very naive question. As far as I understand the folding of a molecule is governed by the electromagnetic forces between its atoms and also between its atoms and the atoms in the surrounding ...
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Thermoregulation Question

I had the following question on an exam of mine and I got it wrong, so I was wondering if someone could help explain the reasoning to me. Below I list my explanation. An overheated and sick dog in ...
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Entropy and Open Systems - AP Biology

I had the following question on an exam of mine and I got the points for the question, but I am wondering if someone could please explain why it is correct, or rather, if it is correct at all: As ...
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Meaning of 'forms of free energy'?

I was doing a practice exam paper and it asked for different 'forms of free energy'. I am a physicist rather then a biologist so 'free energy' to me means Gibb's Free Energy: $$G=H-TS$$ But I cannot ...
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What does these $\Delta \Delta G$ numbers signify?

I was reading a paper and came across this table showing $ \Delta \Delta G$ numbers of different nucleotide sequences in DNA/RNA. I know that $\Delta G$ is free energy and $ \Delta \Delta G$ is ...
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Why do plants produce so much more sugar than they use?

I recently asked the question, "Do plants need O2 to consume energy they've stored via sugar?" to which @canadianer responded, "Yes, plants require oxygen to generate ATP from sugar. However, they ...
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Do plants need O₂ to consume energy they've stored via sugar?

This question came up as I work my way through the answers to another question I just asked. My understanding is that plant photosynthesis looks something like this (though with lots more going on ...
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How does it make thermodynamic sense for photosynthesizers to turn CO₂ into O₂?

My understanding is that animal metabolism consists of exothermic reactions like $$\ce{C6H12O6 + 6 O2 ->6 CO2 + 6 H2O + energy}$$ This makes thermodynamic sense to me. Animals need an exothermic ...
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Thermodynamics of Forming Peptide Bonds

Which of the following shows the correct changes in thermodynamic properties for a chemical reaction in which amino acids are linked to form a protein? A) +ΔH, +ΔS, +ΔG B) +ΔH, -ΔS, -ΔG C) +...
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Kinetic Vs Potential Energy in Biochemical Contexts

This question is causing great confusion in my head. Which of the following is an example of potential rather than kinetic energy? A) the muscle contractions of a person mowing grass B) water ...
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Relationship Between Evolution and the Increase of Entropy of Earth

I was confronted by this question: Biological evolution of life on Earth, from simple prokaryote-like cells to large, multicellar eukaryotic organisms, A) has occurred in accordance with the laws of ...
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A question about the intersection of evolution and thermodynamics

From this 2014 article in Quanta magazine by Natalie Wolchover there is a quote from a physicist with an intriguing idea about evolution: “You start with a random clump of atoms, and if you shine ...
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Why isn't the phosphoglycerate kinase reaction of the glycolysis pathway irreversible?

Step 7 of the glycolysis pathway is the conversion of 1,3-bisphosphoglycerate into 3-phosphoglycerate by the action of the enzyme phosphoglycerate kinase, resulting in the production of 2 ATP ...
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What is an irreversible reaction?

There are reactions with large Delta G negative values. Why these reactions are irreversible? As in: out of 10 steps of Glycolysis, 3 are irreversible steps. I need an explanation for why they are ...
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Why do peas change colour?

I am doing an experiment on preservation of peas. The first notable change to the peas over a period of one week is that they have changed colour from bright green to a dull colour... Why is this so?...
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Doesn't osmosis violate the law of conservation of energy?

Osmosis seems very counter-intuitive to me. I will try to explain my doubt with the following thought experiment: Consider a huge container divided into two by a semi-permeable membrane. We add equal ...
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When a Lysosome's bonding sites all get bonded to, what is the most resource and energy efficient way to handle the used Lysosome?

Let's say a Lysosome that bonds to a hazardous material to neutralize it has all bonding sites used up. would it be more safe / efficient to excrete the entire Lysosome / hazardous material molecule ...
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Why does the hydrolysis of ATP increasing entropy increase the Phosphoryl-­‐transfer Potential?

I am currently taking a biology class. I do not understand this concept. I understand that the electrostatic repulsion of the negative charges, resonance stabilization and hydration stabilization all ...
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How do warm-blooded animals keep their temperatures constant?

Warm blooded animals like us keep their temperature constant irrespective of their surroundings. But how do they do that? Energy should be supplied from the inside. I assume that reactions like making ...
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How to quantitatively measure work done by a biological system?

Thermodynamic efficiency can be expressed as the ratio of Work done(W) to Energy invested (Q). Thermodynamic efficiency= W/Q How can one measure work done by a ...
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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 ...
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How does water buffer a sudden drop in temperature?

A property of water is that it is slow to heat and cool. According to my biology book, some energy from an increase in temperature would spent breaking hydrogen bonds, so that temperature does not ...