Intro to Metabolism (Ch. 8) Flashcards
Define metabolism
The totality of an organism’s chemical reactions
Distinguish between catabolic pathways and anabolic pathways
Catabolic pathways are degradative processes that release energy by breaking down complex molecules into simpler compounds. Ex.: Cellular respiration
Anabolic pahtways consume energy to build complicated molecules from simpler ones. Also called biosynthetic pahtways. Ex.: Synthesis of an amino acid from simpler molecules or of a protein from amino acids.
What are the forms of energy?
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Kinetic energy is the energy of motion
- includes heat or thermal energy – kinetic energy associated with the random movement of atoms or molecules
- light is a type of energy that can do work, like powering photosynthesis
-
Potential energy is energy of location or structure
- like water behind a dam
-
Chemical energy refers to potential energy available for release in a chemical reaction
*
What is the first law of thermodynamics?
Conservation of energy.
The first law of thermodynamics is that the energy of the universe is constant: Energy can be transferred and transformed, but it cannot be created or destroyed.
What is the second law of thermodynamics?
Every energy transfer/transformation increases the entropy of the universe.
During every reaction or energy transfer/transformation, some energy is lost and makes the universe slightly more disordered.
Another formulation: *For a process to occur spontaneously, it must increase the entropy of the universe. *
Define entropy
Entropy is a measure or disorder or randomness.
What is a spontaneous process?
A spontaneous process is one that can occur without an input of energy. It is energetically favorable. Not necessarily instantaneous.
Define the Gibbs free energy of a system. What does free energy mean?
Free energy is the portion of a system’s energy that can perform work with the temperature and pressure are uniform through the system. It is like potential energy.
∆G = ∆H - T∆S
∆G = free energy
∆H = change in the system’s enthalpy
T = Temperature
∆S = change in system’s entropy
Define enthalpy for biological systems
In biological systems, enthalpy is equivalent to total energy
How do we use ∆G to predict a process’s spontanaeity?
If ∆G is negative, the process is spontaneous.
Under what circumstances – according to the equation for Gibbs free energy – is a reaction spontaneous? Also state the equation for Gibbs free energy.
∆G = ∆H - T∆S
∆G < 0 when:
- ∆H < 0 (change total energy is negative, i.e. the system gives up enthalpy and H decreases)
or
- T∆S must be positive (the system gives up order and S increases)
or
- both
Why do biologists care about processes’ spontanaeity (re: Gibbs free energy)?
Because spontaneous processes can be harnessed to do work.
Describe Gibbs free energy in terms of initial/final states.
∆G = Gfinal - Ginitial
When a process involves a loss of free energy during the change from initial to final state, ∆G is negative.
Describe Gibbs free energy in terms of instability
∆G is like a measure of a system’s instability – it’s tendency to change to a more stable state. Unstable (higher G) tend to change in such a way that they become more stable (lower G) – i.e. ∆G < 0.
What is an exergonic vs. an endergonic reaction?
Exergonic - energy outward. Releases free energy. Spontaneous.
Endergonic - energy inward. Absorbs free energy from surroudings. Non-spontaneous
What kinds of work does a cell do?
- Chemical work
- Transport work
- Mechanical work
What is chemical work?
The pushing of endergonic reactions that would not occur spontaneously
What is transport work?
Pumping substances across membranes against the direction of spontaneous movement
Mechanical work
For instance, beating cilia, contracting muscle cells, and moving chromosomes during cellular reproduction.
What is energy coupling?
Energy coupling is a way cells manage their energy resources to do work. They use an exergonic process to drive an endergonic one.
What is ATP? Describe its structure.
adenosine triphosphate. ATP has ribose with the nitrogenous base adenine and a chain of three phosphate groups bonded to it.
Describe the hydrolysis of ATP. What are its effects? How does it work?
Hydrolysis breaks the bonds between ATP’s phosphate groups.
Adding a water molecule breaks off a molecule of inorganic phosphate (HOPO32-) and leaves the ATP, which is now adenosine diphosphate (ADP).
Is ATP hydrolysis exergonic of endergonic? How much energy does it release?
Exergonic.
Why does ATP release so much energy when an inorganic phosphate group is broken off during hydrolysis?
Because all three phosphate groups are negatively charged. These like charges are crowded, and their mutual repulsion makes the ATP molecule unstable. The triphosphate tail is like a compressed spring.
How could you use ATP hydrolysis to couple an enzymatic reaction?
If ∆G of a particular endergonic reaction is less than the amount of energy released by ATP hydrolysis, then the two reactions can be coupled so that, overall, the coupled reactions are exergonic.
Usually, this means you have to couple the phosphate group to some other group, the covalently bonded phosphorylated intermediate.
Which two forms of cell work are most driven by ATP hydrolysis?
- Mechanical work -
- Transport work -
ATP hydrolysis changes the protein’s shape and, often, its binding ability.
What is a phosphorylated intermediate? Why are they important? How do they work?
A phosphorylated intermediate is some molecule that receives a phosphate group from ATP, which are covalently bonded. Forming phosphorylated intermediates is the key to coupling exergonic/endergonic reactions. Phosphorylated intermediates are less stable than the unphosphorylated molecule.
How do you prepare ADP for use again?
You rephosphorylate ADP using energy from other catabolism. Then it can be hydrolized again.
What is an enzyme?
An enzyme is a large protein that acts as a catalyst - a chemical agent that speeds up a reaction without being consumed.
What is activation energy?
Free energy of activation is the initial energy required to contort reactant molecules so that the bonds can break
How do enzymes affect reactions in terms of Ea?
Enzymes lower Ea (but keep Gibbs free energy the same)
What is the active site of an enzyme?
The one part of the enzyme molecule that actually binds to the substrate.
What is induced fit?
Induced fit is the effect that occurs when a substrate enters the active site – the enzyme changes shape slightly and makes the substrate fit even more closely, like a clasping handshake.
What environmental factors affect the activty of an enzyme?
- Temperature - higher temp increases activity up to a point until enzyme is denatured
- pH - there is an optimal pH for activity
- Cofactors - nonprotein helpers that bind to enzymes
- Inhibitors - chemicals that stop the action of an enzyme
What are the types of inhibitors of enzyme activity?
Competitive and noncompetitive
What do you call a case where a protein’s function at one site is affected by the binding of a regulatory molecule to a separate site?
allosteric regulation
What is allosteric regulation? What effect does it have on activity?
When an enzyme’s function is regulated by a regulatory molecule that binds to a separate site on an enzyme. It can inhibit or stimulate activity.
Describe most enzymes that are allosterically regulated
- Typically 2+ subunits, each with its own active site
- Complex oscillates between catalytically active and inactive shapes
Describe allosteric cooperativity. How does it work and what is its effect?
Allosteric cooperativity is when a substrate molecule binding to one active site sets all the other active sites in “active” mode, increasing catalytic activity.
It amplifies the response of enzymes to substrates: one substrate molecule primes an enzyme to act on other substrate molecules more readily.
What is feedback inhibition?
Feedback inhibition is a mode of metabolic controll wherein a metabolic pathway is switched off by the inhibitory binding of its end product to an enzyme that acts early in the pathway.
When end product concentration gets high enough, it binds to the original enzyme and production stops.
