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.

Filter by
Sorted by
Tagged with
-1 votes
1 answer
66 views

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 ...
James Strieter's user avatar
1 vote
0 answers
76 views

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, ...
Maximilian Press's user avatar
0 votes
1 answer
44 views

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]) ...
Hendrix13's user avatar
  • 101
0 votes
1 answer
328 views

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 ...
Bakr Alrawe's user avatar
2 votes
1 answer
194 views

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 ...
The Quark's user avatar
  • 213
2 votes
0 answers
53 views

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 ...
niko papiashvili's user avatar
2 votes
1 answer
184 views

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,...
niko papiashvili's user avatar
-1 votes
1 answer
87 views

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 ...
seamos's user avatar
  • 177
6 votes
1 answer
378 views

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 ...
seamos's user avatar
  • 177
1 vote
0 answers
94 views

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) ...
Anton's user avatar
  • 113
-2 votes
1 answer
139 views

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 ...
Anton's user avatar
  • 113
0 votes
1 answer
733 views

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 ...
An Ignorant Wanderer's user avatar
-3 votes
1 answer
142 views

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 ...
Turk Hill's user avatar
  • 105
2 votes
2 answers
841 views

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 ...
Clay A.'s user avatar
  • 37
5 votes
4 answers
285 views

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 ...
E. Ginzburg's user avatar
2 votes
1 answer
71 views

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.
Ben's user avatar
  • 31
1 vote
0 answers
125 views

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 ...
S.Surace's user avatar
  • 111
1 vote
1 answer
52 views

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?
Bimlendra Ray's user avatar
0 votes
1 answer
1k views

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 ...
Zeyuan's user avatar
  • 103
3 votes
2 answers
468 views

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 ...
ynn's user avatar
  • 133
1 vote
2 answers
128 views

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, ...
justdoit's user avatar
  • 704
2 votes
1 answer
62 views

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 ...
francoiskroll's user avatar
0 votes
2 answers
698 views

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 ...
user avatar
3 votes
2 answers
176 views

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 ...
wuschi's user avatar
  • 163
1 vote
0 answers
553 views

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 ...
user avatar
1 vote
1 answer
1k views

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 ...
Yousif's user avatar
  • 27
2 votes
1 answer
199 views

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 ...
Rafael Franco's user avatar
3 votes
0 answers
3k views

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 ...
flor1an's user avatar
  • 131
5 votes
2 answers
4k views

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 ...
Jonathan Smith's user avatar
5 votes
1 answer
1k views

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 ...
Mike NZ's user avatar
  • 185
2 votes
0 answers
2k views

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 ...
sreekara's user avatar
  • 759
2 votes
1 answer
395 views

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+ +...
Meep's user avatar
  • 2,939
1 vote
3 answers
6k views

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 ...
user avatar
6 votes
1 answer
23k views

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 ...
KingBoomie's user avatar
  • 2,380
4 votes
2 answers
8k views

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 ...
user25269's user avatar
5 votes
1 answer
318 views

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 ...
Probably's user avatar
  • 2,450
8 votes
3 answers
5k views

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 ...
vik1245's user avatar
  • 569
4 votes
4 answers
337 views

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 ...
Reza's user avatar
  • 275
1 vote
2 answers
1k views

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 ...
Aleksandr Hovhannisyan's user avatar
1 vote
2 answers
1k views

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 ...
Aleksandr Hovhannisyan's user avatar
1 vote
0 answers
158 views

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 ...
Quantum spaghettification's user avatar
4 votes
1 answer
3k views

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 ...
dexterdev's user avatar
  • 1,133
1 vote
0 answers
2k views

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 ...
kuzzooroo's user avatar
  • 441
0 votes
1 answer
83 views

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 ...
kuzzooroo's user avatar
  • 441
5 votes
2 answers
192 views

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 ...
kuzzooroo's user avatar
  • 441
3 votes
1 answer
8k views

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, +...
yolo123's user avatar
  • 374
3 votes
3 answers
4k views

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 ...
yolo123's user avatar
  • 374
10 votes
7 answers
3k views

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 ...
yolo123's user avatar
  • 374
13 votes
1 answer
422 views

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 ...
daniel's user avatar
  • 2,799
11 votes
2 answers
11k views

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 ...
katherinebridges's user avatar