Exam 2 Chapter 6 Flashcards
What is thermodynamics?
The study of energy and its transformations
Types of systems
Open, isolated, and closed
All living organisms are ___ systems
Open
What is an isolated system?
Does not exchange matter or energy with surroundings
What is a closed system?
Exchanges energy with surroundings but not matter
What is an open system?
Exchanges matter and energy with surroundings
What is the first law of thermodynamics?
Energy can be transformed from one form to another but cannot be created or destroyed, so total amount of energy in system and surroundings is constant
Second law of thermodynamics
Total disorder/entropy of a system always increases
Kinetic and potential energy
Kinetic energy= energy of motion, potential energy= stored energy depending upon relative position of various parts of a system
What is a spontaneous reaction?
A chemical or physical reaction that will occur without energy input
What makes a reaction spontaneous?
Reactions tend to be spontaneous if the products have less potential energy than the reactants (potential energy is enthalpy)
What are exothermic and endothermic reactions?
Reactions releasing energy are exothermic, reactions absorbing energy are endothermic
What makes a reaction spontaneous in terms of entropy?
Reactions tend to be spontaneous if products are less ordered than the reactants
What is free energy?
The portion of a system’s energy available to do work (G)
The change can be calculated by G=H-TS where H is change in enthalpy and s is change in entropy
For a reaction to be spontaneous, G must be _____
<0
Will reactants always convert completely to products?
No, even in presence of -G. The reactions run in direction of completion until equilibrium is reached. At equilibrium, G=0
T or F: The more negative the G, the further towards completion the reaction will move before equilibrium is established
T
Can living systems reach G=0?
Not truly, because systems are open, products do not accumulate, and supply of reactants is constant, meaning G of life is always negative. G=0 only after death
Can reactions be reversible?
Yes, if delta g is near 0 and amount of products/reactants is changed
Distinguish between endergonic and exergonic reactions
Exergonic- releases energy, g is negative (spontaneous)
Endergonic- reactants must gain energy, so G is positive (nonspontaneous)
What is a metabolic pathway?
A series of reactions in which the products of one reaction are used as the reactants for next reaction
Catabolic pathway or reaction
Energy is released by breaking down complex molecules into simpler ones
Anabolic pathway
Energy is used to build complicated molecules from simpler ones
What is ATP?
Energy currency of cell, energy stored in triphosphate group and breakdown of ATP via hydrolysis drives endergonic reactions.
What is the G of atp becoming ADP and P?
-7.3 so spontaneous
What is energy coupling?
When ATP is hydrolyzed, the terminal phosphate group is transferred to a reactant molecule involved in an endergonic reaction (phosphorylation; the modified molecule is the one being phosphorylated)
What does energy coupling require?
An enzyme with a specific site that binds ATP and react and molecule to bring both in close association
Give an example of energy coupling
A. Without atp, formation of glutamine from glutamic acid and ammonia is not spontaneous (G=3.4)
B. ATP is hydrolyzed, G=-7.3
C. Coupled with ATP hydrolysis, glutamine synthesis is spontaneous since net G is -7.3+3.4 or -3.9 kcal/mol
Glutamyl phosphate and ammonia
Why are redox reactions important?
Involved in energy flow through biological systems since electrons carry energy with them
What is oxidation?
Loss of an electron
What is reduction?
Gain of an electron
What is activation energy?
Energy needed to start a reaction, even a spontaneous one. It makes bonds unstable and ready to be broken
What are enzymes
Catalysts, meaning they lower the activation energy and thus accelerate the reaction
How is the direction of a chemical reaction determined?
By the difference in free energy between products and reactants
Can enzymes change the delta g value?
No, and the enzyme itself is also not altered
What about an enzyme allows it to work on substrates?
3D shape
Are enzymes altered in reactions?
No
The reactant an enzyme works on is called
The substrate
Are enzymes specific?
Yes- only a single type of substrate molecule or group of closely related molecules
What is the active site?
The place where the substrate interacts with the enzyme
What is induced fit?
Induced fit refers to the idea that the enzyme and substrate are distorted after binding, making the chemical bonds ready for reaction since it is less stable
How does sucrase work?
The substrate is sucrose (glucose and fructose) binds to sucrase, which places stress on the glucose-fructose bond. The bond between glucose and fructose then breaks, and products are released.
What are cofactors?
A nonprotein group that binds to the enzyme for catalytic activity; some are metallic ions like iron, copper, magnesium, zinc, manganese, and others are small organic molecules (coenzymes) which are derived from vitamins
What are prosthetic groups?
Tightly bound coenzymes
How do enzymes stabilize the transition state?
Brings reacting molecules together
Exposes reactants to altered change environments that promote catalysis
Change the shape of substrate molecules
How does temperature affect enzymes?
Rate of an enzyme reaction increases w/ temperature, but only to a certain point
How does pH affect enzyme activity?
Ionic interactions hold enzymes together
What factors affect enzyme activity?
Concentration of substrate and binding molecules, control mechanisms, temp, pH
In the presence of excess substrate, the rate of catalysis is _______
proportional to amount of enzyme. if enzyme concentration is kept constant and concentration of substrate increases, rate of catalysis increases until enzymes become saturated
What happens when enzymes are saturated with substrate?
Rate of reaction levels off
What type of inhibitor is aspirin/
A reversible competitive one; it inhibits cyclo-oxygenase
What type of inhibitor is penicillin?
Irreversible competitive
How are enzymes regulated?
Inhibition, allosteric regulation, covalent modification
Competitive inhibitors
Compete with the substrate for the same active site. The competitive inhibitor mimics the substrate and takes its place. It is reversible by increasing amount of substrate
Noncompetitive inhibitors
Bind to the enzyme in a location other than the active site, which causes the enzyme’s shape to change so substrate cannot bind. It is not reversible with more substrate
Allosteric sites
Specific binding sites act as on or off switches; it is reversible and is not involved with the active site. it usually has two conformations, the high-affinity active form and the low-affinity inactive form
Give an example of allosteric feedback inhibition
The threonine isoleucine conversion has four intermediates, and isoleucine goes back to inhibit enzyme 1 (threonine deaminase)
What is feedback inhibition?
The end product goes back and inhibits an enzyme in its production cycle
How are enzymes modified by chemical modification>
Enzymes are regulated by chemical linkage, functional groups, or other molecules. For example, phosphorylation by protein kinases can activate or deactivate an enzyme since protein kinases act on an enzyme; dephosphorylation by phosphorylation reverses the effects
As temperature rises, enzyme activity ____
Increases until H-bonds break and denaturation occurs. Both these effects work together to change enzyme catalysis rates
Give an example of a heat-sensitive enzyme
In siamese cats, the enzyme catalyzing melanin production only works in colder regions which is why only certain parts of siamese cats are black
What are ribozymes and why are they important?
RNA may have been original source of enzymes and informational molecules. Ribozymes accelerate certain biological reactions and also catalyze cutting and splicing reactions that remove noncoding segments from RNA; they also catalyze amino acid linkage.
Does a ribozyme fit the definition of an enzyme?
No, it does not. While ribozymes and enzymes both have catalytic activity, a key difference is that enzymes are protein based, whereas ribozymes are nucelotide based. This means that factors like temperature and pH affect the two molecules differently. Furthermore, whereas enzymes work on a variety of different molecules and situations, ribozymes are specifically tailored to RNA-centric reactions. They are likely less diverse than proteins given that they only have four monomers while proteins have 20.
Where are ribozomes found?
Large subunit
Give an example of a ribozyme
Peptidyl trandferase, in the LSU
Chemical energy
The potential energy that can be released in a chemical reaction
A thermos is a _____ system
isolated
A human is an ________ system
open
the earth is a ____ system
closed
What is the ultimate source of energy?
The sun
If segregated solutes move randomly around and through gaps in the membrane, the system inevitably progress towards ______
higher entropy
The likelihood of order (increases/decreases) as the number of molecules in the system increases
decreases
Energy coupling
Coupling of an exergonic reaction to an endergonic one
is moving away from equilibrium spontaneous or nonspontaneous
nonspontaneous
more exothermic reactions usually have a higher or lower free energy?
lower
T or F: Spontaneous reactions proceed rapidly
F
what do enzymes do?
lower activation energy
What is activation energy?
The input of energy requored to make molecules into a less stable state so breakage can occur. This allows molecules to occupy the transition state
What provides activation energy in chemical reactions?
Kinetic energy from collision
What does cyanide do?
irreversible inhibitor that inhibits cytochrome oxidase, the enzyme catalyzing last step in cellular respiration
What type of inhibitors are antibiotics?
Irreversible inhibitors; toxic metals are also irreversible inhibitors
What is superoxide dismutase?
Turns the superoxide radical into ordinary oxygen and h202 since superoxide is a dangerous byproduct of oxygen metabolism
what are the cofactors of superoxide dismutase
copper and zinc
Corn pollen enzyme ideal temp range
30-32
Arctic snow flea enzyme range
-10
Thermobacillus and thermal bacteria
85 C +
