Bioenegetics Flashcards
Bioenergetics
what is bioenergetics
the study of the transformation of energy in living organisms
what is bioenergetics based on
thermodynamics energy capture energy conversion energy storage biochemistry enzyme kinetics
what is the first law of thermodynamics
energy cannot be created or destroyed - only converted - principle of conservation of energy
what is the second law of thermodynamics
energy transfer increases the entropy of the universe
where does photosynthesis occur
chloroplast
where does cellular respiration occur
mitochondria
what is Gibbs free energy
the portion of energy in a system used to perform work
under what conditions will a reaction proceed in terms of free energy
a reaction will occur spontaneously if it decreases G - that is, delta G is negative
what is an exergonic reaction
spontaneous - one that involves energy release - proceeds with a net release of free energy (G decreases) - deltaG is -ve - the greater the decrease in energy the greater the amount of work that can be done
what is an endergonic reaction
one that requires energy - absorbs free energy - G increases -deltaG is +ve - nonspontaneous - the magnitude of deltaG is the energy required to drive the reaction
where is the chemical energy stored in ATP
in the last phosphate group
in what two ways can ATP be formed
- substrate level phosphorylation (transfer of phosphate group)
- oxidative phosphorylation (proton gradient, ATP synthase)
relocating electrons from sugars (weakly electronegative) to oxygen (strongly electronegative)results in an energy intake/release
release
what is chemiosmosis
movement of ions across a semipermeable membrane, down their electrochemical gradient e.g. the generation of ATP by the movement of H across a membrane
electron transport chain is accompanied by a directional movement of what across the membrane
hydrogen ions
reactions that make and use H gradient are separate and require what characteristic of the membrane
it needs to be intact
name the 4 main parts of ATP synthase
rotor
stator
rod
knob
what is the function of the rotor of ATP synthase
it spins clockwise when H ions flow past it
what is the function of the stator of ATP synthase
holds rotor and knob in position
what is the function of the rod of ATP synthase
turns the rotor and activates the knob
what is the function of the knob of ATP synthase
catalytic sites join phosphate to ADP making ATP
the energy released in an exergonic reaction can be used for what
to trigger endergonic reaction
NAD+ captures electrons from redox reactions and delivers them to what
the electron transport chain
what does the electron transport chain establish across the inner membrane of chloroplasts and mitochondria
a proton gradient
what happens when protons flow back through ATP synthase
ATP is produced
The trans-membrane H+ gradient acts as what between redox potential and ATP synthesis
a ‘high-energy’ intermediate
when proteins are needed sugars can be broken down into what to enable this
amino acids
which process drives cellular economy by extracting energy stored in sugars and other fuels
cellular respiration
what kind of activities do cells use the energy gained by cellular respiration for
e. g. transport of solutes between the cellular interior and the extracellular environment
e. g. changing cell shape
how the single celled marine organisms called dinoflagellates become illuminated
they convert the energy stored in certain organic molecules into light. This process is called bioluminescence
what is metabolism
the totality of an organisms metabolic reactions
each step of a metabolic pathway is catalysed by what
a specific enzyme
what does metabolism control
material and energy resources of the cell
describe a catabolic reaction
a reaction during which larger more complex molecules are broken down into smaller more simpler ones (exergonic reaction) e.g. cellular respiration (sugar/other fuels broken down in the presence of oxygen to form carbon dioxide and water)
The energy that was stored in the organic molecules is released and becomes available to do the work of the cell
can metabolic pathways have more than one starting molecule or product
yes there can be multiple starting molecules and/or products involved in a metabolic reaction
describe anabolic pathways
the reaction of smaller less complex molecules to form larger more complex molecules. These reactions consume energy (endergonic reaction) and are sometimes called biosynthetic pathways
give an example of an anabolic reaction
e. g. amino acid synthesis
e. g. protein synthesis
explain how catabolic and anabolic reactions support each other
the energy released from catabolic reactions can be stored and used to drive the energy consuming anabolic reactions
what is bioenergetics
the study of how energy flows through living organisms
what is kinetic energy
the energy associated with the relative motion of objects
what is thermal energy
kinetic energy associated with the random movement of molecules or atoms
what is heat
thermal energy in transfer from one object to another
is light a form of energy
yes - it can be used to perform work e.g. powering photosynthesis in green plants
can objects that are stationary possess energy
yes - they possess potential energy
what is potential energy
energy that matter possesses because of its location or structure
what is chemical energy
the potential energy available for release in a chemical reaction
complex molecules such as glucose are in high/low chemical energy
high
what is an isolated system
a system that is unable to exchange energy or materials with its surroundings
what is an open system
a system that is able to exchange energy or materials with its surroundings
are organisms open or closed systems
open - they can exchange energy and materials with their surroundings
In most energy transformations some energy is transferred to what type of energy which is then released as heat
thermal energy
During energy transfers from food to an organism very little of the energy is transformed into motion - why is this
most of the energy is lost as heat which dissipates rapidly through the surroundings
the loss of energy as heat by systems makes the surroundings more/less disordered
more - the entropy of the surroundings increases
what is entropy
the measure of disorder - the more disordered the matter the greater the entropy
if a process leads to an increase/decrease in the entropy the process will proceed spontaneously (energetically favourable)
increase
non spontaneous reactions proceed only when what is supplied
energy
living systems increase/decrease the entropy of their surroundings
increase
why is heat energy lost during consumption of food
energy is released to the surroundings during the catabolic reactions that break down the food into its component parts
the energy of the component parts is less than the original food
organisms are islands of low/high entropy in an increasingly ordered/disordered universe
low
disordered
what is gibbs free energy
the portion of a system’s energy that can perform work when temperature and pressure are uniform throughout the system
what is the gibbs free energy of a spontaneous process
negative
what is the gibbs free energy of a non spontaneous process
positive
at what gibbs free energy does a reaction become spontaneous
0
unstable systems have a higher/lower gibbs free energy
higher - they will change in a way to decrease their free energy
when is a reaction said to be at equilibrium
when the forwards and backwards reactions are occurring at the same rate
when a system proceeds towards equilibrium its free energy increases/decreases
decreases - it is becoming more stable
what happens to the gibbs free energy when a system is pushed away from equilibrium
it increases
why do systems never spontaneously move away from equilibrium
any change away from equilibrium has a positive change in free energy and so is not favourable
a process is spontaneous and can perform work only when it is moving towards equilibrium
breaking bonds requires/releases energy
requires
making bonds requires/releases energy
releases
is a living cell in equilibrium
no -there is a constant flow of materials in and out of the cell, preventing pathways from ever reaching equilibrium
animals and other nonphotosynthetic organisms must have a constant supply of free energy in the form of what
organic products of photosynthesis
what are the three main type of work that a cell carries out
chemical work - the pushing of endergonic (nonspontaneous) reactions
transport work - the pumping of substances across membranes against the direction of spontaneous movement
mechanical work - e.g. the beating of cilia, contraction of muscle cells, movement of chromosomes
what is energy coupling
the use of an exergonic process to drive an endergonic one
what are the components of ATP
sugar ribose, nitrogenous base adenine and a chain of 3 phosphate groups
in addition to its role in energy coupling ATP is also a component of which biological molecule
ATP is one of the nucleoside triphosphates used to make RNA
the bonds between each phosphate group of ATP can be broken by what type of reaction
hydrolysis
what happens when the terminal phosphate bond of ATP is broken by hydrolysis
an inorganic phosphate leaves ATP and the ATP becomes ADP
is the reaction below endergonic or exergonic
ATP —> ADP + Pi
exergonic - releases energy
why are the phosphate bonds of ATP sometimes referred to as high energy
Because the hydrolysis of ATP releases energy - ATP and water have high energy relative to the products (ADP + Pi)
where does the energy released in ATP hydrolysis come from
the chemical change of the system to a state of lower free energy - NOT FROM THE PHOSPHATE BONDS
why is ATP useful to a cell
because the energy released on losing a phosphate is larger than the energy most other molecules could deliver
the 3 phosphate groups of ATP are negatively/positively charged
negatively - these like charges are crowded together and their repulsion contributes to the instability of this region
if deltaG of an endergonic reaction is less/more than the amount of energy released by ATP hydrolysis then the two reactions can be coupled so that overall the coupled reactions are exergonic
less than - this usually involves phosphorylation
what is phosphorylation
the transfer of a phosphate group form one molecule to another molecule - the recipient molecule is called the phosphorylation intermediate
a phosphorylated intermediate is more/less reactive than the original unphosphorylated molecule
more reactive (less stable, more free energy)
go over the conversion of glutamic acid to glutamine
the reaction in isolation is endergonic but by coupling with ATP can proceed
- ATP phosphorylates glutamic acid, making it less stable, with more free energy
- ammonia displaces the phosphate group, forming glutamine
ATP hydrolysis changes in what properties of proteins
shape and binding affinities
During transport work what is the effect of ATP hydrolysis
ATP phosphorylates transport proteins causing a shape change that allows transport of solutes
During mechanical work what is the effect of ATP hydrolysis
ATP binds non covalently to motor proteins and then is hydrolysed releasing ADP and Pi causing a shape change that walks the motor protein forward along the cytoskeleton. Another ATP molecule can bind and the process repeats
ATP hydrolysis is anabolic/catabolic
catabolic - energy released - exergonic
ATP synthesis is anabolic/catabolic
anabolic - energy required - endergonic
what is an enzyme
a macromolecule that acts as a catalyst
what is the activation energy
the energy required to start a reaction
what is activation energy often supplied by
heat in the form of thermal energy absorbed for the surroundings
what is the state called when reactant molecules have absorbed enough energy for their bonds to break
transition state
Proteins, DNA and other complex cellular molecules are rich in free energy and have the potential to do what
decompose spontaneously - these molecules only exist because the temperature of a normal cell doesn’t allow enough molecules to reach the activation energy
enzymes lower what of a reaction
activation energy
what is the complex called that occurs when an enzyme and substrate bind
enzyme-substrate complex
what does reaction of sucrose with water and sucrase produce
glucose and fructose
the specificity of an enzyme is a result of what property
its shape - a consequence of its amino acid sequence
what part of the enzyme binds to the substrate
active site - a pocket or groove on the surface of the enzyme
what happens when an enzyme and substrate react
- substrate enters the active site and forms weak bonds (hydrogen bonds, ionic bonds) with the enzyme - this induce a shape change
- additional weak bonds form sue to the shape change causing the active site to enfold the substrate, holding it into place.
the tightening of binding after the initial contact of the enzyme and substrate is called what
induced fit
what part of the active site catalyses conversion from substrate to product
the R groups of a few amino acids that make up the active site
what mechanisms do enzymes use that lower activation energy
- when there are multiple reactants the active site provides a template so the substrates can come together in the correct orientation for reaction
- The enzyme can stretch the substrate towards its transition state form, stressing the bonds to be broken
- active site can provide a microenvironment e.g. the active site may be a pocket of low pH facilitating H+ transfer to the substrate
- amino acid in the active site directly participate in the reaction
when is an enzyme said to be saturated
when adding more substrate does not increase rate
which environmental factors can effect enzyme activity
pH
temperature
presence of detergents
optimal conditions favour the most/least active shape of the enzyme
most active - this is why enzymes work better in optimal conditions
temperature increase speeds up a reaction to a point because the molecules collide more frequently but after a certain point reaction rate drops why is this?
the enzyme becomes denatured - thermal agitation disrupts hydrogen bonds, ionic bonds and other weak interactions that stabilise the active shape of the enzyme
what are optimal conditions for thermophilic bacteria
high temperatures like in hot springs
many enzymes require non protein helpers for catalytic activity, what are these called
cofactors
how are cofactors bound to the enzyme
tightly - as a permanent resident
loosely - reversibly along with the substrate
if a cofactor is an organic molecule what is it referred to as
coenzyme
if an inhibitor attaches to an enzyme via covalent bonds is this reversible
usually yes
what is a competitive inhibitor
an inhibitor that binds to the active site, mimicking the substrate - this can be overcome by increasing thee concentration of the substrate
what is a non-competitive inhibitor
they bind to the enzyme in a place other than the active site which changes the enzymes shape making the active site less effective
toxins and poisons are often reversible/irreversible inhibitors
irreversible
how does a cell control when and where enzymes are active
by switching on and off genes that encode enzymes or by regulating activity once the enzyme is made
what is allosteric regulation
when the proteins function at one site is affected by the binding of a regulatory molecule to a separate site resulting in either inhibition or stimulation of enzyme activity
most allosterically regulated enzymes have how many subunits and active sites
2 or more - the complex oscillates between the active and inactive shapes
how does regulatory molecule binding of one subunit of an allosteric enzyme effect the enzyme as a whole
binding to one subunit changes the shape of the other subunits
what is cooperativity
binding to one active site of a multisubunit complex changes a shape change in all the subunits - this amplifies the response
why is cooperativity considered allosteric regulation
because even though the substrate binds to the active site, its binding effects catalysis in another active site
what is feedback inhibition
a metabolic pathway is altered by the inhibitory binding of its end product to an enzyme that acts early in the pathway
what is a multienzyme complex
a team of enzymes where the product from the first enzyme becomes the substrate for the adjacent enzyme
