-total of an organisms chemical reactions.
-It's an emergent property of life.
-manages the material and energy resource sof the cell
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Metabolic Pathway
answer
-Series of chemical reactions catalyzed by several enzymes
-molecule is altered in a series of steps to get final product
-usually contains specific enzymes
-are catabolic or anabolic
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Catabolic pathways
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-breakdown of food to get energy
-cellular respiration - sugar glucose and other organic fuels are broken down in presence of O2 to CO2 and water and energy
-"downhill" avenues
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anabolic pathways
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-biosynthetic pathways
-consum eenergy to build molecules from simple ones
-uphill avenue
0
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Bioenergetics
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study of how energy flows through living organisms
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what is energy
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-the capacity to cause change
-move matter against forces like gravity and friction
-ability to arrange a collection of matter
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What are the different types of energy?
answer
Thermal - random movement of atoms or molecules
Light - can be used to perform photosynthesis
Chemical - bonds between molecules
Electrical - moving electrons
Nuclear - forces holding subatomic nuclear particles together
Radiant - energy from light
Mechanical - movement on a large scale
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Potential energy
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energy because of location or structure
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Chemical energy is a type of
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-potential energy
-potential energy in the bonds between molecules
-lots of potential energy in forces holding nucleus together
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Kinetic Energy
answer
energy of movement
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Electrical energy is a type of
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kinetic energy - movement of electric charge
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Light energy is a type of
answer
kinetic energy
movement in photons
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Mechanical energy and thermal energy have both
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potential and kinetic energy
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Enthalpy
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total energy of a system, taking into account pressure and volume
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What type of energy do cell snormally use to power their reactions?
answer
chemical
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In thermodynamics, what is the system, and the surroundings?
answer
System - what you are studying
Surrounding - everything else around it
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In thermodynamics, what is an isolated system and an open system?
answer
Isolated - no energy exchange with surroundings
open - can exchange energy bw system and surrounding
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Organisms are isolated or open systems?
answer
Open systems
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What is the first law of thermodynamics?
answer
Energy can be transferred or transformed, but not destroyed.
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What is the second law of thermodynamics?
answer
Every transfer or transformation makes the universe more disordered (increases entropy)
-in the form of heat
-although order increases locally, universe as a whole is increasing in entropy
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What type of energy can't living organisms use? Why?
answer
Living organisms can't use heat because it's
-chaotic
-spread out
-unorganized
-cells are isothermic so no heat gradient for cells to use to generate energy for work
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Why can't cells convert heat to another type of energy?
answer
Living organisms are isothermal
heat moves down its concentration gradient, but in living organisms, there is no heat gradient
only thing organism can do is use heat to maintain optimal working temperatures
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All other forms of energy eventually turn into
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heat energy
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As heat is released into environment, it contributes to
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an increase in disorder
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According to Law 2, what will eventually happen to useable energy in the universe?
answer
The universe will eventually
-run out of usable energy
-there will be no gradients of anything
-there will just be expanding heat
-maximum entropy (disorder)
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Living beings are what types of systems?
answer
They are open systems
-can exchange matter and energy with environment
-generate order within themselves using matter and energy from their environment
-high energy, low entropy
total entropy in universe increases as a result of enregy transformations in cells
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What does free energy change (delta G) tell you about the reaction?
answer
Free energy (delta G) tells us whether or not reaction occurs spontaneously and if it needs heat to happen or gives off heat
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Free energy is
answer
portion of a system's energy that can perform work under stable temp and pressure
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More free energy is
answer
higher G
less stable
but greater work capacity
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Less free energy
answer
lower G
more stable
less work capacity
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Spontaneous change
answer
-Delta G<0 (free energy decreases) - gives up order
-exergonic
-system becomes more stable
-released energy can be harness to do work
-Delta H decreases (gives up enthalpy)
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Equilibrium is
answer
-a state of maximum stability
-rate of the forward equals the rate of the reverse
-no net change in reactants or product concentrations
-any change from equilibrium is not spontaneous, will have a positive delta G
-at equlibrium, reactions stop in closed systems
question
Living systems reach equilibrium
answer
-Never!
-chemical reactions eventually reach equilibrium and then can do no work
-this would be useless for the animal
-so cell is never at equilbrium, forcing reactions to continue producing
-however products never build up (they are used in other reactions) so equilibrium is never reached
-hence, continuous and constant flow of materials in and out keep metabolic pathway from reaching equilibrium
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Living systems never reach equilibrium as long as there is steady supply of what two main reactants?
answer
Glucose and water (for ATP hydrolysis)
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Exergonic reactions
answer
-net release of free energy
-delta G is negative - product G
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Endergonic reactions
answer
-absorb free energy
-stores free energy in molecules of products, G products < G reactants
-delta G increases, therefore positive
-nonspontaneous (requires energy to happen)
-uphill reaction
-usually needs to be coupled with exergonic reaction to happen
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Catabolic pathways in cells do what to free energy?
answer
releases free energy in a series of reactions
they are exergonic
product does not accumulate, so reactions continue to happen
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What is metabolism?
answer
Sum of all chemical reactions that occur in a living organism
question
Catabolism
answer
-breakdown of large molecules into smaller
-exergonic
-releases energy
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Anabolism
answer
-builds large molecules from smaller ones
-usually energonic, absorvs energy
-many cellular reactions are endergonic
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In order to fuel endergonic reactions, cells do what?
answer
Couple with an exergonic reaction, usually hydrolysis of ATP
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What are the three types of work cells do?
answer
Chemical
transport
mechanical
-they do this by coupling reactions with ATP
question
Structure of ATP
answer
three phosphate attached to
ribose which is attached to
adenosine
question
How does ATP hydrolysis release energy?
answer
Water breaks covalent bond between the last phosphate and the second phosphate, releasing energy (7.3kcal/mol. In a cell, -13kcal/mol)
question
How do cells couple energy?
answer
-If delta G of endergonic < delta G of ATP hydrolysis, two reactions can be coupled
-phosphate group is added to some other reactant (reactant becomes phosphorylated)
question
How does ATP coupling work?
answer
-ATP transfers a phosphate group to one of the components of the system
-unstable intermediate is formed
-energy is emitted by releasing the phosphate group drives the reaction
-ATP then is regenerated with a catabolic reaction that phosphorylates ADP to make more ATP
-ATP is created by ATP synthase during photosynthesis in plant from sun energy
question
Enzymes speed up metabolic reactions by
answer
lowering the activation energy of reactions
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Enzymes are
answer
-biological catalysts that speed up the reaction without being consumed
-lower the Ea of reactions by bringing the reaction through different mechanism
-often proteins
question
What is activation energy?
answer
Ea - initial investment of heat energy to start a reaction. It breaks the bonds of the reactants for endergonic and exergonic reactions.
-Cells, molecules are bent, and energy is absorbed
-at the top of the eA summit, reactants hit transition stage before products are formed.
-if Ea is not achieved, no reaction takes place
question
What is the induced fit model?
answer
Enzymes are very specific
bind substrate to it, and it changes shape when substrates are bound
weakens the bonds in the substrate so that reaction doesn't need as much energy to take place
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Enzymes are also
answer
reusable
specific
question
Is the Ea smaller or bigger with an enzyme? Is the rate slower or faster with an enzyme?
answer
Ea is smaller
rate is faster
question
What is the substrate
answer
reactant enzyme reacts on (is specific to enzyme)
question
Substrate complex
answer
-when enxyme binds to its substrate in the active site
-this is intermediary and unstable
-substrate is held in active site by weak h bonds and ionic bonds
-once products are made, enzymes return to original conformation
question
Enzyme mechanisms that lower Ea are
answer
1) active sites provide a template on which the substrates can come together in the right orientation
2) active site clutches at the bound substrate, stretching moelcules towards their transitio state form and reduces the needed free energy for reaction to happen
3) may provide microencironment that is conducive to reaction
question
Enzymes of require
answer
cofactors - help enzymes perform reactions, can be used by reaction
-inorganic coenzymes are ions
organic ones are called coenzymes (vitamins)
-bind to enzyme, help it to conform to its shape
question
RNA polymerase needs Mg2+ to do its job. Mg2+ is a
answer
coenzyme
question
Enzymatic inhibitions is
answer
the binding of non substrate molecules to enzyme, inhibiting its function
question
competitive inhibition is
answer
molecule mimics substrate, binds to active site
this inhibition can be overridden by merely adding more substrate
question
Noncompetitive inhibition
answer
binds to a different site on an enzyme, an allosteric site
enzyme changes shape and is no longer able to have active sites
more substrates do not change inability of enzymes
question
what is reversible inhibition
answer
-used by cell to control reaction rate, is reversible
question
what is irreversible inhibition
answer
poisoning enzyme, permanently binds enzyme
question
Allosteric regulation
answer
case in which aproteins function at one site is affected by binding of regulatory molecule to an allosteric site
question
Allosteric site is
answer
Site that allows for binding of regulatory molecule that is NOT the active site
question
With allosteric regulation, enzyme is
answer
stabilized in active or inactive form and is therefor inhibited or stimulated
-all this binding is reversible
-molecule makes the shape of the enzyme better so it can stimulate catalysis
-worse so that it will not bind to anything
question
Cooperativity
answer
enzyme has two or more subunits, a substrate molecule causing induced fit in one subunit can trigger same shape in other units
-activator that binds to active site stabilizes the form of the other subunits, allowing them to bind better
question
Feedback inhibition
answer
Feedback in metabolic pathway inhibits first enzyme in the pathway
-prevents waste by overproduction
-reversible binding
-usually the last product that inhibits first enzyme
question
Which of the following situations does not represent an energy transformation?
§ the release of carbon dioxide as glucose is broken down during cellular respiration
§ the production of sugars from carbon dioxide and water during photosynthesis
§ the production of ATP using phosphate from the breakdown of glucose
§ coupling of ATP hydrolysis to the production of a proton gradient across a membrane by a proton pump
§ All of the listed responses represent energy transformations.
answer
§ coupling of ATP hydrolysis to the production of a proton gradient across a membrane by a proton pump
question
Consider the growth of a farmer's crop over a season. Which of the following correctly states a limitation imposed by the first or second law of thermodynamics?
§ The entropy of the universe must decrease to account for the increased entropy associated with plant growth.
§ Growth of the crops must occur spontaneously.
§ To obey the first law, the crops must represent an open system.
§ The process of photosynthesis produces energy that the plant uses to grow.
§ All of the listed responses are correct.
answer
§ To obey the first law, the crops must represent an open system.
question
Which is the most abundant form of energy in a cell?
answer
Chemical energy
question
Which of the following is an example of the second law of thermodynamics as it applies to biological reactions?
§ The aerobic respiration of one molecule of glucose produces six molecules each of carbon dioxide and water.
§ All types of cellular respiration produce ATP.
§ Cellular respiration releases some energy as heat.
§ The first and second choices are correct.
§ The first, second, and third choices are correct.
answer
§ The aerobic respiration of one molecule of glucose produces six molecules each of carbon dioxide and water.
question
• According to the second law of thermodynamics, which of the following is true?
§ The decrease in entropy associated with life must be compensated for by increased entropy in the environment in which life exists.
§ Energy conversions increase the order in the universe.
§ The total amount of energy in the universe is constant.
§ All reactions produce some heat.
§ The entropy of the universe is constantly decreasing.
answer
§ The decrease in entropy associated with life must be compensated for by increased entropy in the environment in which life exists.
question
• Which types of molecules have the greatest free energy?
answer
Starch molecules
question
• The electronic arrangement in which of the following molecules means that this (these) molecule(s) has/have greater free energy than the others?
§ methane
§ carbon dioxide
§ water
§ The first two molecules listed are roughly equal in the energy they contain.
§ The first three molecules listed are roughly equal in the energy they contain.
answer
methane
question
• If, during a process, the system becomes more ordered, then _____.
answer
§ ?S is negative (disorder decreases)
question
• From the equation ?G = ?H - T?S it is clear that _____.
§ a decrease in the system's total energy will increase the probability of spontaneous change
§ increasing the entropy of a system will increase the probability of spontaneous change
§ increasing the temperature of a system will increase the probability of spontaneous change
§ The first and second choices are correct.
§ The first three choices are correct.
answer
§ The first three choices are correct.
question
• Metabolic pathways in cells are typically far from equilibrium. What tend(s) to keep these pathways away from equilibrium?
answer
§ the continuous removal of the products of a pathway to be used in other reactions
§ an input of free energy from outside the pathway
question
• How do enzymes lower activation energy?
answer
§ By locally concentrating reactants
question
• A plot of reaction rate (velocity) against temperature for an enzyme indicates little activity at 10°C and 45°C, with peak activity at 35°C. The most reasonable explanation for the low velocity at 10°C is that _____.
answer
§ There is too little activation energy at 10 degrees.
question
Enzyme activity is affected by pH because _____.
answer
§ high or low pH may disrupt hydrogen bonding or ionic interactions and thus change the shape of the active site
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