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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Can Sleeping With Reptiles Reduce Excess Body Heat from Your Partner? [closed]
I'm an engineer and biology is my weakest point, so please forgive if this question is dumb.
My wife always complains that I set the air temperature too cold at night. She's exothermic in a number of ...
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Compute a melting temperature in viennaRNA?
Posting here to get views, but may be more appropriate for bioinformatics or chemistry SE.
There are a variety of utilities such as biopython or primer3 that compute melting temperatures.
However, ...
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How can combusted methane from landfill samples be quantified? [closed]
Background:
For my studies I'm wanting and attempting to make a landfill greenhouse gas emissions (GHG) model that predicts the amount of greenhouse gas equivalent emissions ($GHG_{eq}$ [tonnes/year]) ...
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Why do catabolic reactions release heat despite that breaking bonds absorbs heat?
According to Campbell, the definition of a catabolic reaction is:
Some metabolic pathways release energy by breaking down complex
molecules to simpler compounds. these degradative processes are ...
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Are there irreversible metabolic reactions that can happen in opposite ways depending on the cellular conditions?
Irreversible reactions are thermodynamically irreversible, not microscopically irreversible. "Irreversible" here means the reaction happens "out-of-equilibrium". It is a ...
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Thermodynamics of one directional passive membrane transporters
I have read in my biochemistry textbook, that some membrane transporters transport only in one direction, moreover, they don't require ATP energy. I wonder, why these proteins do not act as ...
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Thermodynamics of passive transport
My question is, where does energy come from for passive translocase's conformational changes? I argue it can't be concentration gradient, as concentration is only statistical phenomenon at micro scale,...
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Contradiction between random molecular collisions and regulated cellular processes [closed]
A cell is a chemical system, consisting of billions of molecules, ions, and atoms. These chemical species are constantly engaged in chemical reactions.
Physics gives the impression that chemical ...
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Thermodynamically, how did the first cell arise?
Living cells are biochemical systems that constantly perform chemical reactions. One of the important consequences of these chemical reactions is the capacity of a living cell to replicate itself. The ...
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Why protons flow back to the matrix through ATP synthase?
I am reading oxidative phosphorylation and I can't understand why the protons that are pumped out must go again into the matrix and finally produce ATP.
Suppose initially that the inside (Matrix-M) ...
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What favors the active transport in a membrane? [closed]
I was reading about active transport in membranes where ATP is used. ATP "reacts" with the protein pump and converts into ADP and also make a conformational change to the pump. Now this ...
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Activated carrier molecules and their relationship to enzymes
I am reading Molecular Biology of the Cell, and one thing I don't quite get is the difference between an enzyme and an activated carrier molecule. I understand that enzymes lower the activation energy ...
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A question about entropy and Thermodynamics
According to the Second Law of Thermodynamics (also known as the laws of conversation of energy and mass), anything is an isolated system cannot increase in complexity. For example, a wearing suit ...
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Understanding entropy and the second law of thermodynamics as involved in metabolic processes
My AP biology textbook, (the 10th edition of Campbell Biology) states entropy as being the disorder or randomness of the atoms involved in any matter, but Khan Academy says that this example isn't ...
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Why does protein folding not depend on the order in which it is synthesized?
I read an article recently, written by researcher from Department of Biochemistry, University of Washington, which stated that:
Similarly, success in de novo protein design bears on the question I ...
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Speed of reaction vs equilibrium
Does increasing the speed of a reaction (say by introducing a catalyst) shift the equilibrium of the reaction? I assume it does not, as Gibbs free energy is not changed, but I am not sure.
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What is the status of the "Free Energy Principle" as a theory of living organisms?
The free energy principle states that biological organisms maintain their order by minimizing a function called variational free energy (VFE).
While it is the case that the minimum to VFE also ...
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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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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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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 is 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
NADP+ +2H+ +...
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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) +ΔH, -ΔS, +...
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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 ...