Download AP Bio ch 6

Chapter 6
An Introduction to Metabolism
- all of an organism’s chemical processes
- 2 types of metabolic pathways:
catabolic pathways - release energy
- break down complex molecules into simpler ones
- example:
cellular respiration breaking glucose down
into CO2and H2O providing cell with energy
anabolic pathways
- consume energy
- build complex molecules from simpler ones
- examples: photosynthesis making glucose from CO2
and H2O
polymerization reactions
energy - capacity to do work
metabolism
kinetic energy - energy of motion
- energy in the process of doing work
- examples:
- heat (thermal energy)  random movement of molecules
- light energy from sun  powers photosynthesis
potential energy
- energy matter possesses because of its location or arrangement
- examples:
- a ball at the top of a hill or water behind a dam (due to gravity)
- chemical energy stored in molecules because of arrangement of
nuclei and electrons
energy can be transformed from 1 type to another:
examples:
- in photosynthesis, the kinetic energy of sunlight is transformed into potential energy
of chemical bonds
- when burning gasoline, the potential energy of chemical bonds is transformed into kinetic
energy which pushes engine pistons
thermodynamics
- study of energy transformations
first law of thermodynamics - energy can be transferred and transformed, but it can’t be created or
destroyed
second law of thermodynamics
- every energy transfer or transformation makes the universe more
disordered (increases entropy of universe)
entropy
- designated S
- measure of disorder (proportional to randomness)
closed system - collection of matter under study which is isolated from its surroundings
open system - system in which energy can be transferred between the system and its surroundings
The entropy of a system may decrease, but the entropy of a system plus its surroundings must always
increase.
organisms
- highly ordered yet do not violate the second law
- maintain highly ordered structure at the expense of increased entropy of their surroundings
- take in high energy molecules and extract chemical energy to create and maintain order
- return simpler low energy molecules (CO2, H2O) and heat to surroundings
enthalpy
- total energy of a system
- not all is available to do work
free energy
- amount of energy in a system that is available to do work
- designated G
G = H – TS
G – free energy
H – total energy (enthalpy)
T – temperature (Kelvin)
S – entropy
∆G
- change in free energy
- change in free energy from the initial state to the final state of a reaction
∆ G = ∆ H – T∆ S (at constant temperature and pressure)
∆ G – change in free energy
∆ H – change in total energy (enthalpy)
T – temperature (Kelvin)
∆ S – change in entropy
free energy
- indicates whether a reaction will occur spontaneously or not
spontaneous reaction - a reaction that will occur without additional energy
- free energy decreases (∆ G < 0)
- can occur with a decrease in enthalpy (∆ H) or an increase in entropy (∆ S)
higher temperature
- greater kinetic energy of molecules disrupts order ( random collisions)
- enhances effect of an entropy change
high energy systems - unstable
- tend to change to a more stable state with a lower free energy
free energy and equilibrium
- as a reaction approached equilibrium, ∆ G decreases (spontaneous reaction)
- when a reaction is pushed away from equilibrium, ∆ G increases (non-spontaneous reaction)
- when a system reaches equilibrium, ∆ G = 0 (no net change in the system)
exergonic reaction
endergonic reaction
- proceeds with a net loss of ∆ G (∆ G is negative)
- products have less free energy that reactants
- spontaneous reaction
- proceeds with a net gain of ∆ G (∆ G is positive)
- requires input of energy
- products have more free energy than reactants
- non-spontaneous reaction
If a chemical process is exergonic, the reverse process must be endergonic.
example:
cellular respiration is an exergonic process
2870 kJ (686 kcal) of energy are released from each mole of glucose in
respiration (∆ G = -2870 kJ/mol or ∆ G = -686 kcal/mol)
photosynthesis is an endergonic process
2870 kJ (686 kcal) of energy must be added to produce a mole of glucose in
photosynthesis (∆ G = + 2870 kJ/mol
metabolic disequilibrium
or
∆ G = +686 kcal/mol)
- necessary for life
- if metabolic reactions reach equilibrium, the cell dies (∆ G = 0, no work
can be done)
- metabolic reactions are “pulled forward” because their products become
reactants for the next reaction in the metabolic pathway
ATP
- adenosine triphosphate
- immediate source of energy that drives most cellular work including:
mechanical work (cilia beating, muscle contraction, etc.)
transport work (pumping substances across membranes)
chemical work (endergonic reactions like polymerization)
ATP
- nucleotide with unstable phosphate bonds
- phosphate bonds are hydrolyzed to yield energy for endergonic reactions
components of ATP: adenine (nitrogenous base)
ribose (5 carbon sugar)
3 phosphate groups
phosphate bonds
- unstable
- can be broken (exergonic reaction)
- when terminal phosphate bond is hydrolyzed, a phosphate group is removed
producing ADP
ATP +
H2O 
ADP +
Ⓟ
- releases about 31 kJ/mol (7.3 kcal/mol) under standard conditions
(∆ G = -31 kJ/mol or ∆ G = -7.3 kcal/mol)
- exergonic reaction (products more stable than reactants)
How ATP performs work:
exergonic hydrolysis of ATP is couple with endergonic reactions
a phosphate group is transferred to another molecule
phosphorylated molecule becomes more reactive
example:
conversion of glutamic acid to glutamine
Glu
+
NH3

Gln
(∆ G = +14.2 kJ/mol)
(endergonic rection)
2 step process:
1) hydrolysis of ATP & phosphorylation of Glu (becomes unstable)
Glu
+
ATP 
Glu-Ⓟ
+
ADP
2) replacement of phosphate group with ammonia
Glu-Ⓟ +
NH3 
Gln
+
Ⓟ
overall ∆ G: Glu
ATP
+
NH3

Gln
∆ G = +14.2 kJ/mol

ADP
+
Ⓟ
∆ G = -31.0 kJ/mol
net ∆ G
- 16.8 kJ/mol
(overall process is exergonic)
regeneration of ATP - endergonic reaction: ADP + Ⓟ  ATP (∆ G = +31 kJ/mol)
- occurs rapidly (107 molecules are used and regenerated in each cell every second)
- energy required comes from the exergonic process of cellular respiration
enzymes
A chemical reaction will occur spontaneously if it releases free energy (-∆ G), but it may occur too slowly to
be effective in living cells  biochemical reactions require enzymes to speed up and control reactions.
catalyst
- chemical agent that speeds up a reaction without being permanently changed in the process
- can be used over and over
enzymes
- biological catalysts made of protein
- speed up reactions by lowering energy barriers
activation energy
- amount of free energy reactant molecules must absorb to start a reaction (EA)
- needed to break chemical bonds
transition state - unstable condition of reactants that have absorbed enough free energy to react
exergonic reaction:
- reactants must absorb enough energy (EA) to reach the transition state (top of hill)
- usually involves absorption of thermal energy from surroundings
- reaction occurs and energy is released as new bonds form (downhill portion)
- ∆ G for overall reaction is the difference between the free energy of products and reactants
- free energy of products is less than reactants in an exergonic reaction
breakdown of biological macromolecules
- exergonic
- cannot absorb enough energy to reach transition state
- need enzymes
enzymes
- lower EA
- transition state can be reached at cellular temperatures
- very selective for the reaction they will catalyze
substrate
- substance an enzyme acts on (made more reactive)
- catalyzed to product after it binds to active site of enzyme
enzyme + substrate  enzyme-substrate complex  product + enzyme
enzyme
- specific for a certain substrate
- 3-D shape determines specificity
active site
- region of enzyme which binds to substrate
- formed by a few amino acids
- fits compatibly with substrate
induced fit
- change in shape of active site which is induced by the substrate
catalytic cycle of enzymes:
1.
substrate binds active site (E-S complex forms)
substrate held in active site by weak interactions
2.
induced fit of active site around substrate
side chains of a few amino acids in active site catalyze conversion of substrate to product
3.
product(s) leave active site
enzyme emerges unchanged (can be used over and over)
Ways enzymes lower activation energy to speed up reactions:
- active site may hold reactants in proper position to react
- induced fit of active site may distort substrate’s chemical bonds (less energy needed to break them)
- active site may provide a micro-environment conducive to particular reaction types (example: acidic
side chains may lower pH in the active site which allows particular reaction to occur)
- amino acid side chains in active site may participate directly in reaction
substrate concentration
higher substrate concentration = faster reaction (to a point)
- enzyme can become saturated with substrate if concentration of substrate gets high enough
(active sites of all enzymes molecules are filled)
- when saturated, reaction rate depends on how fast active sites can convert substrate to product
- when enzyme is saturated, reaction rate may be increased by adding more enzyme
effects on enzyme activity
effect of temperature
optimal temperature (35oC to 40oC in humans) allows greatest number of molecular collisions
without denaturing enzyme
( temperature =  kinetic energy =  collisions =  reaction rate)
beyond optimal temperature, reaction rate slows as enzyme denatures
( thermal energy disrupts weak bonds in enzymes)
effect of pH
optimal pH range for most enzymes is 6 – 8
some operate best at more extremes of pH (stomach enzyme pepsin works best at pH 2)
effect of cofactors
cofactors
- small, nonprotein molecules needed for proper enzyme function
- may bind to active site or active site and substrate
- some are inorganic (zinc, iron, copper, etc.)
- some are organic and called coenzymes (vitamins)
effect of enzyme inhibitors
some chemicals may inhibit enzyme activity
irreversible inhibition - inhibitor attaches by covalent bonds
reversible inhibition - inhibitor attaches by weak bonds
competitive inhibitors - resemble substrate
- compete with substrate for active site (block site from substrate)
- overcome by increasing substrate concentration (if reversible)
noncompetitive inhibitors
Control of Metabolism:
- bind to another part of enzyme molecule causing it to change
shape (active site can’t bind substrate)
- may act as toxins (DDT, antibiotics)
- increasing substrate concentration won’t overcome this
allosteric regulation
feedback inhibition
cooperativity
allosteric regulation
- controls metabolism
allosteric enzymes
- have 2 shapes:
active conformation
inactive conformation
allosteric site - receptor site on some part of enzyme molecule (other than active site)
- activator binds here stabilizing active conformation of enzyme
- noncompetitive inhibitor binds here stabilizing inactive conformation
feedback inhibition
- metabolic pathway regulated by its own end product
- end product inhibits an enzyme somewhere in the pathway
cooperativity - substrate molecules may enhance enzyme activity
- substrate binds to active site of 1 enzyme subunit causing a shape change that
enhances substrate binding at active site of other subunit(s)