Chapter 8 - An Introduction to Metabolism Flashcards
what does an organism metabolism do?
An organism’s metabolism transforms matter and energy and is subject to the laws of thermodynamics
what is catabolism?
- break things down
- fueling reactions (breakdown of glucose)
- energy is released
- generate more building blocks for biosynthesis
what is anabolism?
- build things up
- the synthesis of complex organic molecules from simpler ones
- requires energy from fueling reactions (usually ATP)
what is energy?
the capacity to cause change
what are the different forms of energy?
1) thermal
2) kinetic
3) potential
4) chemical: potential energy available for release in a chemical reactions
what is thermodynamics?
the study of the energy transformations that occur in a collection of matter
what kinds of systems are organism?
open systems!
can exchange energy and matter
what is the first law of thermodynamics?
energy can be transferred and transformed but it cannot be created or destroyed (it’s constant)
how is energy often lost?
unusable energy is often lost as heat
what is the second law of thermodynamics?
every energy transfer or transformation increases the entropy (disorder) of the universe
what is a spontaneous reaction?
if a process:
- increases in entropy
- proceeds without requiring an input of energy
means its energetically favorable
things in nature strive for high entropy, low enthalpy
what is free energy?
the portion of a system’s energy that can perform work when temperature and pressure are uniform throughout the system as in a living cell
what is ∆H?
change in enthalpy
what is ∆S?
change in entropy
∆G
The change in free energy (ΔG) during a process is related to the change in enthalpy or change in totally energy (H), change in entropy (S), and temperature in Kelvin (T)
when is a reaction spontaneous?
- ∆G
- ∆H
+ ∆S
values of ∆G
∆G < 0 spontaneous rxn
∆G > 0 not spontaneous
what is an exergonic reaction?
- energy released
- spontaneous
- reactants have higher energy than products
(ΔG < 0)
what is an endergonic reaction?
- energy required
- nonspontaneous
- products have higher energy than reactants
(ΔG > 0)
what is chemical equilibrium?
the rate of the forward reaction equals the rate of the reverse and neither is favored (ΔG = 0)
what are the three different kinds of work?
1) chemical work
2) transport work
3) mechanical work
what is energy coupling?
the use of an exergonic process to drive an endergonic one
ATP is responsible for mediating most energy coupling in cells and acts as immediate source of energy
what is ATP?
adenosine triphosphate
contains: ribose sugar, nitrogenous base adenine, and three phosphate groups
used to make RNA
what happens when ATP is hydrolyzed?
bonds between phosphate groups of ATP can be broken by hydrolysis –> a molecules of inorganic HOPO3^-2 leaves the ATP which becomes ADP
ATP + H2O –> ADP + Pi
exergonic reaction: releases 7.3 kcal/mol ATP
releases energy because all three phosphate groups are negatively charged and crowded together = repulsion
how does hydrolysis of ATP perform work?
the heat/energy released during ATP hydrolysis is harnessed by the cell’s proteins to perform chemical, transport, and mechanical work
when can reactions be coupled?
if the ∆G of an endergonic reaction is less than the amount of energy released by ATP hydrolysis then the two reactions can be couples so that overall the coupled reactions are exergonic
what is the phosphorylated intermediate?
the recipient molecule of the phosphate group from hydrolysis of ATP is called the phosphorylated intermediate
more reactive/less stable than the original unphosphorylated molecule
transport work and ATP hydrolysis
1) ATP is bound noncovalenty to motor protein
2) ATP is hydrolyzed
3) another ATP molecule can then bind
at each stage the motor protein changes its shape and ability to bind the cytoskeleton resulting in movement of protein along cytoskeleton
regeneration of ATP
ATP is renewable: it is regenerated by the addition of a phosphate to ADP (phosphorylation)
ATP synthesis requires energy –> energy required comes from exergonic breakdown reactions (catabolism) in the cell (such as cellular respiration)
what is an enzyme?
a macromolecule that acts as a catalyst – most are proteins, some are RNA
not a reactant, they aren’t used up
how do enzymes lower the Ea of a reaction?
- Induced fit: binding brings functional groups of the enzyme closer to the substrate and enhances catalysis
- Proper orientation of substrates
- Straining bonds (stabilize transition state)
- Providing favorable environment for the reaction
- Covalently binding the substrate (functional groups participate in reaction)
cannot change ΔG of a reaction*
what is a substrate?
the react that an enzyme acts on
enzyme binds to its substrate and forms an enzyme-substrate complex
what is the active site?
a restricted region of the enzyme molecule that actually binds to the substrate
the pocket/grove where catalysis occurs
How would an enzyme catalyze an endergonic reaction?
By coupling the energy from ATP hydrolysis to the unfavorable reaction
what effects enzyme activity?
Temperature and pH
affect the shape and folding (therefore activity)
what are cofactors?
many enzymes need these nonprotein helps for catalytic activity
may be bound to enzyme as permanent residents or they may bind loosely and reversibly along with the substrate
usually inorganic: metal atoms in ionic form (Zn+2)
if organic –> cofactors
what is a coenzyme?
if a cofactor is an organic molecule it’s referred to as a coenzyme
ex. vitamins, NAD+
what are competitive inhibitors?
they reduce the productivity of the enzymes by blocking the substrates from entering the active sights - mimics the shape of the substrate
can be overcome by increasing the concentration of the substrate so that there’s more substrate than inhibitor b/c noncovalent bonds = not strong
what are noncompetitive inhibitors?
do not directly compete with the substrate to bind to the enzyme at the active site - instead they impede enzymatic reactions by binding to another part of the enzyme which causes the molecule to change its shape in such a way that the active site becomes less effective at catalyzing the conversion of the substrate to product
nonequivalent bonds - not strong
what is allosteric regulation?
the term used to describe any case in which a protein’s function at one site is effected by the binding of a regulatory molecule to a separate site
may result in either inhibition of or stimulation
it’s saying we have a lot of the product to inhibit production, no reason for cell to keep breaking down glucose
what is feedback inhibition?
a pathway’s end product acts as an inhibitor of an enzymatic step earlier in the pathway
localization of enzymes within the cell
the cell is compartmentalized and cellular structures help bring order to metabolic pathways
teams of enzymes for several steps of a metabolic pathway are assembled into a multi-enzyme complex (some are fixed in location and act as structural components)
