Ap Bio Chapter 8

Front 1

• Metabolism

Back 1

the totality of an organism’s chemical reactions

Front 2

• Metabolic pathway

Back 2

begins with a specific molecule which is then altered in a series of defined steps which results in a certain product→ enzymes catalyze each step in the pathway

Front 3

• Catabolic pathways

Back 3

metabolic pathways that release energy by breaking down complex molecules into simpler compounds
o Cellular respiration

Front 4

• Anabolic pathways

Back 4

consume energy to build complicated molecules from simpler ones (aka biosynthetic pathways)
o Ex: Synthesis of proteins from amino acids

Front 5

• Bioenergetics

Back 5

study of how organisms manage their energy resources

Front 6

• Energy

Back 6

capacity to cause change
• Energy can be used to do work (move matter against opposing forces)

Front 7

• Kinetic energy

Back 7

energy in movement

Front 8

• Heat/Thermal energy

Back 8

kinetic energy associated with the random movements of atoms or molecules

Front 9

• Potential energy

Back 9

→ energy due to position/structure

Front 10

• Chemical energy

Back 10

potential energy available for release in a chemical reaction
o Reactants in catabolic RXNS are high in chemical energy

Front 11

• Thermodynamics

Back 11

study of the energy transformations that occur in a collection of matter

Front 12

• System

Back 12

the matter under study

Front 13

• Surroundings

Back 13

→ the rest of the universe and everything outside the system

Front 14

• Closed system

Back 14

the matter under study is isolated from its surroundings

Front 15

• Open system

Back 15

energy and matter can be transferred between the system and its surroundings

Front 16

• First law of thermodynamics

Back 16

→ the energy of the universe is constant
o Energy cannot be created or destroyed
o Aka principle of conservation of energy

Front 17

• Second law of thermodynamics

Back 17

every energy transfer or transformation increases the entropy of the universe. In order for a process to occur spontaneously it must increase the entropy of the universe


o Most energy in an energy transfer becomes unusable energy (heat) so some energy is “lost”
o The loss of usable energy during energy transfer makes the universe more disordered

Front 18

o Entropy

Back 18

measure of disorder or randomness

o The more randomly arranged a collection of matter is the greater its entropy
o There is an unstoppable trend toward randomization of the universe as a whole


• Examples of increasing entropy-→ buildings decay, people age, a burning log
• In order for a process to occur on its own (without energy) it must increase the entropy of the universe

• Living systems increase the entropy of their surroundings

Front 19

• Spontaneous

Back 19

processes that occur without an input of energy
o Things roll downhill

Front 20

• Nonspontaneous

Back 20

processes that require energy
o Things cannot roll uphill

Front 21

• Living systems increase the entropy of their surroundings

Back 21

• Organisms take in organized forms of matter and energy from their surroundings and replace them with less ordered forms
o Ex: animal eats food and breaks the food down into CO2 and H20 (small molecules that store less chemical energy than the food did)
o Depletion of chemical energy is accounted for by heat generated during metabolism


• Evolution of biological order is consistent with the laws of thermodynamics
o Its true that organisms evolved from simpler organisms to more ordered organisms
o The entropy of individual organisms decreased b/c of evolution
o BUT the total entropy of the universe increased- so it fits with the laws of thermodynamics

Front 22

• Energy flows into an ecosystem in the form of ___ and leaves in the form of ___

Back 22

LIGHT

HEAT

Front 23

• Gibbs free energy equation

Back 23

o ΔG = ΔH – TΔS
• ΔG= G final state – G initial state

o G=Free energy
o H=change in enthalpy (aka total energy)
o S=change in entropy
o T=absolute temperature in Kelvin (K= Celcius + 273)

Front 24

• Processes with a negative G

Back 24

are spontaneous

• Every spontaneous process decreases the system’s free energy (b/c G is negative)

Front 25

Processes with positive G

Back 25

• Positive and zero G reactions require energy

Front 26

Which systems tend to have a higher/lower G?

Back 26

• Unstable systems (higher G) tend to change to become more stable (lower G)
o Ex: glucose tends to break down into monomers

• Systems will move toward greater stability (equilibrium)

Front 27

• Equilibrium

Back 27

state of maximum stability

o Reactions proceed to a point where the forward and backward reactions occur at the same rate (said to have reached equilibrium- no further net change in relative concentration of products/reactants)
o Free energy of reactants/products mixture decreases as something moves towards equilibrium
o Free energy increases when the reaction gets pushed away from equilibrium



Systems NEVER spontaneously move away from equilibrium

• Processes are spontaneous and can preform work only as they’re moving towards equilibrium

Front 28

• Exergonic reaction

Back 28

proceeds with a net release of free energy

o Delta G is negative b/c it loses free energy
o Exergonic RXNs occur spontaneously b/c delta G is negative
o Magnitude of delta G for an exergonic reaction represents the maximum amount of work the RXN can perform


cellular respiration is exergonic

Front 29

• Endergonic reaction

Back 29

→ absorbs free energy from its surroundings
o Delta G is positive because it gains energy
o These reactions are nonspontaneous
o Magnitude of delta G is the quantity of energy needed to drive the RXN


synthesizing proteins is endergonic

Front 30

• If a RXN is exergonic in one direction

Back 30

than its reverse reaction is endergonic (and vis versa)

o If this isn’t true than the reaction can’t be reversible

Front 31

• Delta G for cellular respiration

Back 31

-686 kcal/mol

Front 32

• Types of work that a cell does

Back 32

o Mechanical work→ movement
o Transport work→ actively transporting things across the membrane
o Chemical work→ synthesizing polymers with the help of energy

Front 33

• Energy coupling

Back 33

use of an exergonic process to drive an endergonic one
o The way cells manage their energy resources to do work
o ATP is responsible for mediating most energy coupling in cells
o ATP acts as the immediate source of energy that powers cellular work

Front 34

• ATP

Back 34

o Ribose sugar, adenine, and three phosphate groups
o Bonds between phosphate groups in ATP’s tail can be broken by hydrolysis
o Becomes ADP when it loses a phosphate group
o Delta G of ATP→ADP reaction is -7.3 kcal/mol

Front 35

How does ATP generate energy?

Back 35

• Release of energy during ATP hydrolysis comes from the chemical change to a state of lower free energy NOT from the phosphate bonds


phosphorylation

Front 36

• Why does ATP have energy

Back 36

all three phosphate groups are negatively charged and they repel each other and have potential energy

Front 37

• Phosphorylation

Back 37

the transfer of a phosphate group from ATP to a reactant
o The recipient of the phosphate group is said to be phosphorylated
o Phosphorylation makes the reactant unstable and thus more reactive

• The whole process is spontaneous and exergonic

Front 38

Regeneration of ATP

Back 38

• Adding a phosphate group to ADP regenerates ATP

• Free energy required to phosphorylate ADP comes from exergonic break down reactions in the cell
• ATP reactions are reversible so the reaction from ADP→ATP makes 7.3 kcal/mol
o Reaction from ATP→ ADP loses 7.3 kcal/mol


• ADP→ATP reaction is not spontaneous- that’s why you need cellular respiration

Front 39

• Catalyst

Back 39

chemical agent that speeds up a reaction without being consumed by the reaction

organisms use catalysts to provide the activation energy (not heat)

Front 40

• Enzyme

Back 40

catalytic protein

• Enzymes catalyze a reaction by lowering activation energy barrier which enables the reactant molecules to absorb enough energy to reach the transition state
• Enzymes don’t change the delta G of a RXN- they can’t make an endergonic reaction exergonic
• Enzymes speed up reactions that would happen even without the enzyme
• Enzymes determine which chemical reactions will go on in a cell at any particular time


• Enzymes always catalyze the reaction in the direction of equilibrium

Front 41

• Activation energy

Back 41

amount of energy needed to start a reaction- energy required to contort the reactants so the bonds can change
o Amount of energy needed to push the reactants over an energy barrier


often comes in the form of heat
o Absorption of thermal energy increases the speed of the reactant molecules so they collide more often
o Thermal agitation makes the bonds more likely to break


• Activation energy provides a barrier that determines the rate of the reaction
o Reactants must absorb enough energy to reach the top of the activation energy barrier
o If the activation energy is low the reaction will proceed more often

Front 42

• Transition state

Back 42

the state when the reactants are ready to start reacting→ when the reactants have absorbed the required amount of activation energy

Front 43

• Substrate

Back 43

reactant an enzyme acts on


• Enzymes are very specific to their substrates

• Specificity of an enzyme results from its shape

Front 44

• Active site→

Back 44

region where the enzyme bonds to the substrate

Front 45

o Induced fit

Back 45

brings chemical groups of the active site into positions that enhance their ability to catalyze the chemical reaction
• The active site changes shape to accommodate the substrate

Front 46

• Steps in how enzymes work

Back 46

o Substrate enters active site
o Enzyme changes shape so its active site embraces the substrates (induced fit)
o Substrate held in active site by weak bonds like hydrogen bonds and ionic bonds
o Active site (and R groups of its amino acids) lower activation energy and speed up RXN
o Substrates are converted into products
o Products are released
o Active site is now available for new substrates

Front 47

• Ways that enzymes lower activation energy and speed up RXN

Back 47

o Active site provides a template for substrates to come together in the proper orientation
o Active site clutches the bound substrates and stresses the chemical bonds that must be broken in the RXN- distorting the substrate makes it approach the transition state faster
o Active site provides a microenvironment that is more conducive to the reaction→ the active site might have an acidic or basic environment for example
o The active site could directly participate in the chemical RXN

Front 48

• An enzyme is saturated when

Back 48

it’s working the fastest that it can- when the substrate concentration exceeds the enzyme’s capability of processing substrate

o When an enzyme population is saturated the only way to make it go faster is to add more enzyme

Front 49

o Optimal conditions

Back 49

enzymes work under certain specific conditions
o Temp and PH influence enzyme activity

o Enzymes don’t work at very high temps b/c they get denatured

o Generally, High temps (up to a certain point) and neutral PH’s help enzymes work better

o Digestive enzymes work better at acidic PH’s

Front 50

Cofactors

Back 50

non protein helpers for catalytic activity- bind to enzymes to help enzymes out

Front 51

• Coenzyme

Back 51

cofactors made out of organic molecules (C, H, O, N)

Front 52

• Competitive Inhibitors

Back 52

resemble the normal substrate molecule and compete for admission into the active site to inhibit enzyme productivity
o Reduces productivity by blocking active site

Front 53

• Noncompetitive inhibitors

Back 53

impede enzymatic reactions by binding to another part of the enzyme- causes the enzyme to change shape which makes its active site less productive

Front 54

• Selective inhibition

Back 54

cells naturally regulate enzyme activity by making enzyme inhibitors- essential to the control of cellular metabolism

Front 55

• Allosteric regulation

Back 55

any case in which a protein’s function at one site is affected by the binding of a regulatory molecule to a separate site
o Like noncompetitive inhibitors
o Can result in stimulation or inhibition of enzyme activity

Front 56

Allosteric enzymes

Back 56

o composed of multiple sub units and has two conformational states (one active and one inactive)

Front 57

o Allosteric site/Regulatory site

Back 57

the area where the inhibiting or activating regulatory molecule binds to

o A single activator or inhibitor molecule that binds to one regulatory site will affect the active sites of all subunits

Front 58

o Activator

Back 58

bonds with the allosteric site to trigger the active part of the enzyme

Front 59

o Inhibitor

Back 59

bonds with the allosteric site to trigger the inactive part of the enzyme

Front 60

• ATP and allosteric enzymes

Back 60

• ATP binds to catabolic enzymes allosterically and lowers its affinity for substrate and thus inhibiting its activity
• ADP binds to catabolic enzymes and serves as an activator (a major function of catabolism is to generate ATP)
• Allosteric enzymes help regulate the generation of ATP→ if there’s too much ATP the ATP will bind allosterically and slow the catabolic enzymes down…if there’s too much ADP the ADP will bond allosterically and speed up the catabolic enzymes
o Allosteric enzymes control the rate of key reactions in metabolic pathways

Front 61

• Cooperativity

Back 61

→ substrate molecule binding to one active site may stimulate the catalytic powers of a multi subunit enzyme by affecting other active sites
o A substrate molecule causing induced fit in one subunit can trigger the same favorable conformational change in the other sub units
o Helps to amplify the response of enzymes to substrates

Front 62

• Feedback inhibition

Back 62

common method of metabolic control, a metabolic pathway is switched off by the inhibitory binding of its end product to an enzyme that acts early in the pathway
o High concentration of product inhibits the reaction from going faster
o The reaction operates according to how much product is needed
o Ex: as isoleucine accumulates it slows down its own synthesis by allosterically inhibiting the enzyme for the first step of the metabolic pathway
o Prevents the cell from synthesizing too much product