2_1 Flashcards
catabolism vs anabolism
- Catabolic pathways release energy by breaking down complex molecules into simpler compounds.
Cellular respiration, the breakdown of glucose in the presence of oxygen, is an example of a pathway of catabolism. - Anabolic pathways consume energy to build complex molecules from simpler ones. (ex glucose anabolism)
The synthesis of protein from amino acids is an example of anabolism.
potential energy
Potential energy is energy that matter possesses because of its location or structure.
Being on top of the platform, the energy within the bonds of glucose.
kinetic energy
Kinetic energy is energy associated with motion.
Climbing up the ladder, a beating flagellum.
heat energy
Heat (thermal energy) is kinetic energy associated with random movement of atoms or molecules.
open system
In an open system, energy and matter can be transferred between the system and its surroundings.
Organisms are open systems.
The First Law of Thermodynamics
According to the first law of thermodynamics, the energy of the universe is constant.
Energy can be transferred and transformed,but it cannot be created or destroyed.
The first law is also called the principle of conservation of energy.
The Second Law of Thermodynamics
During every energy transfer or transformation, some energy is unusable, and is often lost as heat.
According to the second law of thermodynamics
Every energy transfer or transformation increases the entropy (disorder) of the universe.
- ex: the conversion of chemical energy in food to kinetic energy is inefficient, resulting in the generation of heat and the waste products CO2 and H2O
entropy
A measure of the disorder or randomness of a system.
The more randomly arranged a collection of matter is, the more entropy it has.
- a block of salt has less entropy (has a more organized structure) than a pile of salt (more dispersed).
- a protein molecule has less entropy than the individual amino acids that make it up.
To lower the entropy of a system (make it more organized) requires an input of energy.
entropy of biological systems
- Biological systems usually have great order (low randomness), and therefore exist in a state of low entropy.
- To maintain this state of low entropy requires a constant expenditure of energy: a biological organism is an island of low entropy in a universe of increasing entropy.
- An organism can only be maintained by constantly using energy to reduce its entropy (maintain its order).
free energy
Free energy (G). The amount of energy in a system that is available to do work. G = Gibbs Free Energy
A ordered system (i.e. has a low degree of entropy) has a greater amount of free energy.
deltaG = Gproducts - Greactants
exergonic vs endergonic rxn
exer:
- energy released
- spontaneous
- deltaG < 0
- reactants have higher free energy than prodcuts
ender:
- energy required
- nonspontaneous
- deltaG > 0
- reactants have lower free energy than products
in a spontaneous change,
- higher to lower free energy
- less to more stable
- more to less work capacity
- the released free energy can be harnessed to do work
- ex: gravitational motion, diffusion
The Structure and Hydrolysis of ATP
- ATP is composed of ribose (a sugar), adenine(a nitrogenous base), and three phosphate groups.
- The bonds between the phosphate groups of ATP’s tail can be broken by hydrolysis (HD,DP hydrolysis depolymerization).
- Energy is released from ATP when the terminal phosphate bond is broken (the reaction is exergonic).
The Regeneration of ATP
- ATP is a renewable resource that is regenerated by addition of a phosphate group to adenosine diphosphate (ADP).
- The energy to phosphorylate ADP comes from the catabolism (breakdown) of energy-containing bonds of macromolecules (e.g. glucose).
- Hydrolysis of ATP provides energy to perform cellular work (for endergonic processes)
ATP powers cellular work by
- coupling exergonic reactions to endergonic reactions.
- ATP drives endergonic reactions by phosphorylation, transferring a phosphate group to some other molecule, such as a reactant.
The recipient molecule is now called a phosphorylated intermediate.
A cell does three main kinds of work
(all endergonic)
Chemical
Transport
Mechanical
transport work
ATP hydrolysis leads to a change in transport protein shape and binding ability.
mechanical work
ATP hydrolysis leads to a change in motor protein shape and binding ability.
- ATP binds noncovalently to motor
proteins and then is hydrolyzed. (This moves a vesicle, attached to a motor protein, along a cytoskeletal track.)
enzymes
- Enzymes speed up metabolic reactions by lowering energy barriers (lowering EA).
- A catalyst is a chemical agent that speeds up a reaction without being consumed by the reaction. They do not cause reactions that could not ordinarily occur.
- An enzyme is a catalytic protein.
- Hydrolysis of sucrose by the enzyme sucrase is an example of an enzyme-catalyzed reaction.
activation energy
- Every chemical reaction between molecules involves bond breaking and bond making.
- The initial energy needed to start a chemical reaction is called the free energy of activation, or activation energy (EA).
- Even exergonic reactions need to get over the activation energy “hump”.
- The energy for this is often supplied in the form of thermal energy that the reactant molecules absorb from their surroundings.
- EA is the difference in free energy btwn reactants in the transition state (highest) and reactants at the beginning (lower)
How Enzymes Speed Up Reactions
- Enzymes catalyze reactions by lowering the EA barrier.
- Enzymes do not affect the change in free energy (∆G); instead, they hasten reactions that would occur eventually.
- EA w/ enzyme is LOWER
- Course of rxn w/o enzyme has higher “hump” than w/ enzyme
substrates
- Enzymes bind specific reactant molecules called substrates.
- Substrates bind to a specific site on the enzyme surface called the active site, where catalysis takes place.
- Some enzymes are very specific. They bind specific substrates and catalyze particular reactions under particular conditions
hexokinase
adds a phosphate group to glucose
The catalytic cycle of an enzyme (steps)
- substrates enter active site; enzyme changes shape such that its active site enfolds the substrates (induced fit)
- in this enzyme-substrate complex, substrates are held in active site by weak interactions, such as H bonds and ionic bonds
- active site can lower EA and speed up a rxn
- still in the active site, substrates are converted to products
- products released
- active site available for new substrate molecules
How do enzymes alter the activation state of a reaction?
At the active sites enzymes and substrates interact by breaking old bonds and forming new ones. Enzymes catalyze reactions using one or more of the following mechanisms:
1) Enzymes can orient substrates.
2) Enzymes can add charges to substrates.
3) Enzymes can alter the shape of the substrates.
- Enzymes can orient substrates.
- While free in solution, substrates move randomly. So the probability for an interaction at the angle necessary to change chemical interactions is low.
- When bound to enzymes, two substrates can be oriented in such a way that a reaction becomes more likely.
2) Enzymes can add charges to substrates.
- The R groups (side chains) of an enzyme’s amino acids may directly participate in making substrates more chemically reactive.
- Some enzymes work by acid-base catalysis: acidic or basic side chains of amino acids form the active site and transfer H+ to or from the substrate, destabilizing a covalent bond in a substrate.
3) Enzymes can alter the shape of the substrates.
The stretching of the bonds decreases their stability, making them more reactive.
Competitive inhibitors
bind to the active site of an enzyme, competing with the substrate.
Noncompetitive inhibitors
bind to another part of an enzyme, causing the enzyme to change shape and making the active site less effective.
Allosteric regulation of enzyme activity
- Allosteric regulation occurs when a regulatory molecule binds to a enzyme at one site and affects the enzyme’s function at another site.
- Allosteric refers to an action at a site “other” than the active site.
- Enzymes that are allosterically regulated usually consist of multiple subunits each with its own active site
cooperativity
- Cooperativity is a form of allosteric regulation that can amplify enzyme activity.
- One substrate molecule primes an enzyme to act on additional substrate molecules more readily.
- Cooperativity is allosteric because binding by a substrate to one active site affects catalysis in a different active site.
Metabolism is organized into
- Metabolism is organized into sequences of enzyme-catalyzed chemical reactions called pathways.
- Each step A to B to C to D occurs appropriately because of enzymes. For example, one enzyme converts A to B; a second enzyme converts B to C
feedback inhibition
In feedback inhibition, the end product of a metabolic pathway shuts down the pathway.
Feedback inhibition prevents a cell from wasting chemical resources by synthesizing more product than is needed.
feedback inhibition example
- threonine (the initial substrate) binds to active site on enzyme, threonine deaminase.
- this sets of a string of reactions involving many different phosphorylated intermediates. the end product of these reactions is isoleucine
- isoleucine binds to allosteric site. this is the feedback inhibition – this makes the active site unavailable, halting the pathway
- after isoleucine is used up by the cell, the active site is available once more
