thermodynamics Flashcards
Define and classify systems/surroundings at multiple levels of organization?
A system is a group of interacting or interrelated entities that form a unified whole. It can refer to groups of cells, organisms, or even ecosystems where components function together for a common purpose.
Surroundings: The surroundings, often called the environment, are comprised of all external things outside the system
What are the three different types of systems?
isolated system
closed system
open system
What is an isolated system?
does not exchange matter or energy with its surroundings
What is a closed system?
exchanges energy with its surroundings
What is an open system?
exchanges both energy and matter with its surroundings
are biological systems considered open systems explain the reason why.
Yes, they are; once they exchange matter with their surroundings, matter can enter and leave the system. Ex. plants absorb water, CO2, and nutrients from the environment and release oxygen.
2. energy transfer: biological systems are constantly exchanging energy with their surroundings
etc. organism absorb energy from their surroundings (like sunlight for plants or food for animals) and release energy back into the environment in various forms like heat
3. they are always exchanging energy and matter with their surroundings
What is the difference between matter and energy?
Matter: anything that has mass and takes up space (volume). It is what things are made of. Standard states of matter include solids, liquids and gases.
Energy: the capacity to do work or cause change. Energy can be transferred or converted but cannot be created or destroyed.
Why do biological systems need energy?
Need it to grow and maintain its structure,
1. cellular respiration and ATP production: The primary reason organisms need energy is to fuel cellular processes. In cells, the molecule ATP serves as the primary energy currency; through cellular respiration, cells convert nutrients (mainly glucose) into ATP.
2. Growth and repair: Cells need energy to divide and grow.
3. Active transport: cells often need to move substances against their concentration gradients, which requires energy—for example, the sodium-potassium pump.
Define energy; differentiate between kinetic/potential energy and provide examples of each in biological systems.
Energy is the capacity to do work or the ability to cause change. Energy can neither be created nor destroyed but can be transformed from one to another… the first law of thermodynamics.
Kinetic energy: The energy of motion. An object ( or organism or system) that is in motion
Examples in a biological system:
- molecular movement: at the cellular level, the movement of molecules from higher concentration to lower concentrations.
- Another example can be muscle contractions: muscle fibres contract due to the sliding of actin and myosin filaments against each other.
- active transport: transport proteins move ions or molecules across cell membranes against the concentration gradient. The movement, powered by ATP, is kinetic energy
Potential energy is stored energy; it’s the energy an object (or organism or system has because of its position or state, which has the potential to be converted to kinetic energy.
Examples in biological systems:
1. chemical energy in molecules: The bonds in molecules like glucose or ATP store energy. When these bonds are broken during metabolic reactions, the energy is released and can be used for cellular work. The stored energy in chemical bonds is a form of potential energy.
2. concentration gradients: the cell membrane might maintain ion gradients, such as higher sodium concentration outside the cell than inside. This concentration difference stores potential energy. When ion channels open, allowing ions to flow down their concentration gradient, this potential energy is converted to kinetic energy.
Explain why chemical bonds and electrons are essential forms of potential energy in cells.
chemical bonds as potential energy:
- Storage and release: the energy stored in chemical bonds, especially in molecules like glucose and ATP, represents a significant reserve of potential energy. When these bonds are broken, the stored energy is released and can be harnessed for various cellular functions
- metabolic pathways: fundamental metabolic pathways, such as glycolysis, the Krebs cycle, and oxidative phosphorylation, involve breaking and forming chemical bonds. The energy transitions are crucial for ATP synthesis, which powers most cellular processes.
- A building block of molecules:
The formation and breaking of chemical bonds are essential for biosynthesis. For instance, nucleic acids, proteins, lipids, and carbs are synthesized by forming bonds between smaller molecules.
- ELECTRONS AS POTENTIAL ENERGY:
- Redox rxn: the transfer of electrons in redox (reduction-oxidation) reactions is a central theme in cellular metabolism. As electrons move from one molecule to another ( from glucose to oxygen during cellular respiration), energy is transferred and can be captured and stored as chemical energy in ATP
- Electron transport chain: in eukaryotic cells, the inner mitochondrial membrane houses a series of protein complexes that facilitate the transfer of electrons. This electron transport chain creates a proton gradient, another potential energy used to synthesize ATP.
-Photosynthesis:
In plants and certain microbes, the energy of sunlight is used to excite electrons in chlorophyll and other pigments. These excited electrons possess higher potential energy and are transferred through a series of carriers, ultimately driving the synthesis of ATP and NADPH molecules. Both of these are then used in the Calvin cycle to fix CO2 into glucose, storing energy in its chemical bonds.
WHY is ATP said to be the primary energy currency of all cells, and its role in cells?
It is often referred to as the primary energy currency of all cells due to its fundamental role in storing and transferring energy to drive various cellular processes.
- energy transfer: When a cell needs energy, it breaks down ATP into ADP and a phosphate group. This reaction released the energy stored in the bond between the second and third phosphate groups of ATP. This energy can then be used to power other cellular processes.
- phosphorylation: ATP can donate its terminal phosphate group to another molecule in phosphorylation. This can activate or deactivate enzymes and other proteins, allowing the cell to regulate various processes.
- driving endothermic reactions: some cellular reactions require energy to proceed. ATP provides the necessary energy if it wouldn’t naturally occur
Describe how energy is stored across the membrane.
By maintaining a difference in ion concentration on the two sides of that membrane. This creates an electrochemical gradient, which is a form of potential energy.
-Mitochondria & Cellular Respiration:
Proton Gradient in Mitochondria: As cells break down glucose and other molecules for energy via cellular respiration, high-energy electrons are transferred through a series of proteins in the mitochondrial inner membrane known as the electron transport chain (ETC).
Chemiosmosis: As these electrons move down the chain, specific protein complexes in the ETC actively pump protons (H+) from the matrix into the intermembrane space. This creates a high concentration of protons in the intermembrane space and a lower concentration in the matrix, setting up an electrochemical gradient.
ATP Synthesis: This proton gradient stores potential energy. Protons flow back into the matrix through a protein called ATP synthase due to their electrochemical gradient. This flow of protons provides the energy for ATP synthase to phosphorylate ADP into ATP, which is a key energy currency for the cell.
What are the first and second laws of thermodynamics, and explain how they apply to biological systems
Simple Explanation: Energy cannot be created or destroyed, only transferred or transformed from one form to another.
Application to Biological Systems: When organisms consume food, they don’t “create” energy. Instead, they transform the chemical energy in the food into other forms of energy, such as kinetic energy for movement or thermal energy for heat. The total amount of energy remains constant; it just changes form.
Simple Explanation: Whenever energy is transferred or transformed, some of it becomes unavailable to do work and often dissipates as heat. In other words, every energy transfer increases the disorder or randomness (called “entropy”) of the universe.
Application to Biological Systems: When organisms use energy, not all of it is efficiently used for useful work. Some energy is always lost as heat. This is why when you exercise, your body gets warm. Also, while cells organize molecules in a structured manner (decreasing entropy locally), they increase the overall entropy of their surroundings by releasing heat and waste products.
What is the difference between endergonic and exergonic?
Exergonic:
Energy Change: These reactions release energy.
ΔG (Change in Gibbs Free Energy): For exergonic reactions, ΔG is negative, meaning the products have less free energy than the reactants.
Examples: Cellular respiration is an exergonic process where glucose is broken down, releasing energy.
Spontaneity: Typically, exergonic reactions are spontaneous, meaning they naturally occur without the continuous input of energy.
Endergonic:
Energy Change: These reactions require an input of energy.
ΔG (Change in Gibbs Free Energy): For endergonic reactions, ΔG is positive, meaning the products have more free energy than the reactants.
Examples: Photosynthesis is an endergonic process where energy from sunlight is used to convert carbon dioxide and water into glucose.
Spontaneity: Endergonic reactions are not spontaneous; they need an external energy source to proceed.
Define enthalpy
It is a measure of the total energy of a system. It includes both the internal energy and the energy associated with the volume and pressure of the system. In chemical reactions, the change in enthalpy (ΔH) represents the heat absorbed or released by a reaction at constant pressure.
If ΔH is negative, the reaction is exothermic (releases heat).
If ΔH is positive, the reaction is endothermic (absorbs heat).
Describe connected and couples reactions and explain how they are used in biochemical pathways.
Connected reactions refer to a series of reactions where the product of one reaction becomes the substrate for the following reaction. This is common in metabolic pathways, where the product of one enzyme-catalyzed reaction is used as a substrate by another enzyme in a subsequent step.
In glycolysis, glucose is converted to glucose-6-phosphate by the enzyme hexokinase. This glucose-6-phosphate is then used as a substrate for the next enzyme, phosphoglucoisomerase, to produce fructose-6-phosphate.
COUPLED REACTION :
- involve two or more simultaneous reactions in which a spontaneous reaction (exergonic) drives a non- spontaneously (energonic) to proceed.
-ATP (adenosine triphosphate) hydrolysis is a classic example of an exergonic reaction often coupled to other cell endergonic reactions. The energy released from the hydrolysis of ATP to ADP and inorganic phosphate is used to power other reactions or processes that require energy, such as muscle contraction or the synthesis of biomolecules.
write a metabolic process as a series of connected and coupled reactions
Connected reaction:
Glucose-6-phosphate—->Fructose-6-phosphate
COUPLED REACTION:
- Glucose + ATP—> Glucose–6-phosphate+ADP
Explain how substrate and product concentrations can be manipulated to make a reaction occur.
- Equilibrium Le chatelier’s principle:
Every reversible reaction has an equilibrium constant, which is defined as the ratio of the concentration of products to the concentration of reactants as an equilibrium
- according to le Chatelier’s principle, if you increase the concentration of substrates, the equilibrium will shift towards the side of the products to counteract the products. (Removing them) can also drive the reaction forward.
Coupling with Favorable Reactions:
2.An endergonic reaction (requires energy) can be made to proceed by coupling it with an exergonic reaction (releases energy). This is often seen with reactions that are coupled to ATP hydrolysis. By pairing an unfavorable reaction with the breakdown of ATP, the overall process becomes favorable.
3.Reaction Rate and Kinetics:
Increasing the concentration of a substrate generally increases the rate of a reaction because there are more molecules available to participate in the reaction. However, in enzymatic reactions, once the enzyme’s active sites are saturated with substrate, further increases in substrate concentration won’t significantly increase the reaction rate.
