GB1: Chapter 8 Flashcards
Metabolism
Totality of organism’s chemical reactions; manages materials and energy resources of cell
is an emergent property due to the organized interactions between molecules
Metabolic Pathway
certain molecule is changed in a series of defined steps, each catalyzed by enzyme, to make product
Enzyme
macromolecule that speeds up chemical reaction (lowers activation energy of rxn)
Catabolic pathways (w/ ex)
process that releases energy by breaking down complex molecules into simpler compounds
some bonds are broken/formed, releasing energy, products have lower-energy
- ex: cellular respiration (breaks down glucose and other organic fuels to get water and co2; the energy stored in the organic compounds now can be used)
Anabolic pathways/biosynthetic pathways (w/ ex)
process that consumes energy to form complicated molecules from simpler ones
- ex: creation of polypeptide from amino acids
bioenergetics
study of how energy flows through living organisms
Energy
capacity to cause change/to do work/ability to rearrange collection of matter
kinetic energy
energy of movement of objects (energy the object has due to its motion)
Thermal energy
total kinetic energy of random movement of atoms/molecules
Heat
transfer of thermal energy from one object to another
Potential energy
energy that matter has due to its location or structure
(think of a dam; water has high potential energy because of its altitude above sea level)
Chemical energy
potential energy available for release in chemical reaction
Thermodynamics
study of energy transformation occurring in collection of matter
kinetic energy to potential energy example divers
kinetic energy of muscle movement is being transformed into potential energy as diver gets higher in altitude by climbing ladder
system, surroundings, isolated system, open system
- system: matter under study
- surroundings: everything outside system
- isolated system: system cannot exchange matter/energy with surroundings
-open system: system can exchange matter/energy with surroundings
organisms are what kind of system?
open system: they absorb energy (light energy or chemical energy via organic molecules) and then release heat and metabolic waste products (like co2) to surroundings
1st law of thermodynamics/principle of conservation of energy
energy can be transferred and transformed, but it cannot be created or destroyed
(ex: plant acts as energy transformer bc it absorbs light energy and converts it to chemical energy)
2nd law of thermodynamics
sum of entropies of system and surroundings (the universe) must always increase
entropy
measure of molecular disorder/randomness
(more randomly arranged a collection of matter is = greater entropy)
entropy in universe
increasing amounts of heat, less ordered forms of matter
Spontaneous/energetically favorable process
process that leads to increase in entropy, doesn’t take an input of energy, is ENERGETICALLY FAVORABLE
some are instantaneous and some aren’t
nonspontaneous/nonenergetically favorable process
process that leads to decrease in entropy, requires an INPUT of energy
however, some of that input of energy is lost as heat which also increases entropy into surroundings in universe as a whole
Increase in organization…
does not go against 2nd law of thermodynamics of continual increase in entroy
Gibbs free energy
portion of system’s energy that can do work when temperature/pressure are uniform throughout system
deltaG = deltaH - TdeltaS
deltaH = enthalpy (total energy)
deltaS = entropy (measure of how energy is distributed in a system)
T = temp. in K
delta G = Gfinal - Ginitial
energetically favorable/spontaneous reactions for gibbs
delta G is negative (deltaH is negative or deltaS is positive, or both)
every spontaneous process decreases the system’s free energy
+ deltaG or 0 delta G =
+ deltaG = nonspontaneous (not energetically favorable)
0 deltaG = never spontaneous
system + surroundings
= universe
entropy + analogy
there is always tendency for higher entropy
bedroom over time gets messy, doesn’t suddenly become neat
exergonic reaction
proceeds with net release of free energy
since system lost energy, deltaG is - and rxn is spontaneous/energetically favorable
In larger scale, energy flows into ecosystems in… and exits in…
the form of light; the form of heat
3 main things cell does
chemical work
transport work
mechanical work
chemical work
pushing endergonic reactions that would not occur spontaneously
transport work
pumping of substances across membranes against direction of spontaneous movement
mechanical work
beating of cilia, contraction of muscle cells, movement of chromosomes during cell division
energy coupling
use of exergonic process to drive endergonic one (overall process would be exergonic)
ATP adenosine triphosphate
sugar ribose
nitrogenous base adenine
3 phosphate group chain
hydrolysis of ATP
hydrolysis of ATP with water yields energy, ADP, phosphate group
release of energy is from chemical change of high free energy ATP to lower free energy of ADP
energy is not found in the bonds themselves
the high energy found in especially phosphate groups is due to its higher energy relative to the products (ADP & phosphate group)’s lower energy
Phosphorylation
transfer of phosphate group to molecule from ATP
phosphorylated intermediate
molecule that got phosphorylated (has a phosphate group that was covalently bonded from ATP); has more free energy and less stable
this is how exergonic and endergonic rxns are coupled!
Glutamic acid conversion to glutamine
- is endergonic rxn so needs input of energy (+ deltaG)
- Glutamic acid is phosphorylated by ATP, making it less stable with more free energy
- now ammonia is able to bind to glutamic acid by displacing phosphate group, and ADP and phosphate group come out of reaction. now we have glutamine!
- although deltaG was +, overall is -deltaG because of ATP hydrolysis (which has -deltaG). so with the help of ATP hydrolysis, the overall rxn is spontaneous
ATP cycle
energy released by catabolic rxns is used to fuel energy needed to phosphorylate ADP to make ATP. then when ATP is hydrolyzed, it releases energy needed for anabolic reactions
Activation energy
amount of energy needed to convert reactants to products, is supplied in the form of heat through thermal energy that reactants absorb from surroundings. This heat causes more collisions among substrates and enzymes, which increases the rate of the reaction
catalysis
process where catalyst selectively speeds up a reaction without itself being consumed (alternative to heat since there’s a limit to temperature for living organisms)
transition state
when molecules have absorbed enough free energy, unstable and ready to break bonds
can enzyme change nature of reaction?
NO. enzymes cannot make endergonic rxns exergonic, cannot change deltaG
induced fit
tightening of binding after initial contact; enzyme shape changes slightly because of interactions between enzyme’s active site amino acids and substrate’s.
mechanisms that enzymes use to speed up reactions
- proper orientation to make sure active site correctly binds to substrate in a way so that the right parts can interact and make a product
- puts stress and bends on covalent bond of substrate to break bonds
- provides different microenvironment suitable for specific rxn
- temporarily covalently bond, usually with amino acids
cofactors
nonprotein helpers for catalytic activities; usually for chemical processes like e- transfers
-binds tightly to enzyme as or loosely to substrates
-inorganic: metals
-organic: vitamins - COENZYMES
competitive inhibitors
