mod 6 chap 6 Flashcards
Metabolism
carbon is backbone of organic molecules that make up cells adn cells often use carbon based copmoudsn to store energy
how organsims obtain enegry and carbon is fundemental that it prvoides metabolic classification of life
organisms have two ways of harvesting eenrgy from their envinrment and two sources of carbon - 4 princple wasy organsism acquire enegry and materials
phototrophs
organisms that capture enegry from sunlight
plants are common example
sugars like glucose conain eengry in chem bonds that can be used to syntheize ATP which in turn can pwoer work of cell
chemotrophs
other organisms derive their energy directly from chem compounds
animals are example
they ingest other organisms obtaining glucose that they break down - chem bonds contain energy that is converetd to enegry carried in bonds of atp
autotrophs
organsim can be classfied based on carbon source
some organisms can convert co2 into glucose an organic form of carbon
self feeders
plants
heterotrophs
other organisms obtain carbon from organic molecules syntehsized by other ogranisms
tehse organisms eat other organisms or molecules derived from other organisms
other feeders
animals
metabolism
encopases teh set of chemical rxns that convert molecules into other molecules and transfer energy in living organisms
catabolism is teh set of chem rxns that break down moelcules into smaller units and in the process produce atp
analbolism is ste of chem rxn sthat build molecules from smaller units and require an input of energy in form of ATP
ex. breaking down carbs and amcronmoeces is catabolic while building them in anabolic
Energy
energy is important in biological systems becasue its needed to do work
kinetic enegry is energy of motion - its ascoiated with any kind of moveemnt
potential enegry is stored energy - dpeends on strcuture of object or its position to a field andd its reelased by. a change in the objects structure or position ex. electrochemical gradient is potentail energy
enegry can be coneverted form one form to anotehr
chemical energy
form of potential eengry held in chem bonds between pairs of atoms in a moelcule
covalent bonds form whne sharing of e- between two atoms reuslts in a more stable config - the more stable the more lower potential energy - energy is reuried to break a covalent bond because its going from a lower enegry state to a higher one which requires input of energy
energy is relased when covlanet bonds form
strong bonds are hard to break beacsue teh arrangemnt of orbitals in tehse moelcules is much more stable than if the two atoms didnt share e- - this stable arrangemnt means not a lot of enegry is required to keep it toegther so they dont contain much chem eenrgy
some covalent bonds are weak - easly broken because its not that stable - lots of enegry needed to keep these bonds so they contain lot of chem energy
organic molecules are a source of chem emerngy and called fuel moelcules becasu etehy contain weak covalent bonds
ATP
chem energy in macrmolecules is harnessed by cells to do work
cells dont use this enegry all at once
though series of chem rxns collectly called celuular resipration, they package tjis enegry into a chem form thats accesible to cell - ATP is a form
chem enegry in ATP is used to drive many cellular processes
ATP serves as gobetween acting as intermediary between fuel moelcules that store a large amount of potential eenrgy in their bonds and the activties of teh cell that require an input of energy
atp made of adenosine - base adenine and ribose sugar - ribose atatched to triphosphate
the use of atp as enegry source in nearly all cells reflects it use early in evolution of life on earth
accesible chem enegry of ATP held in bodsn conencting phosphate groups
at cell pH these phospahtes are neg charged and repel eachotehr so the bonds conencting them contain a lot of energy - this enegry is released when new more stable bonds are formed that contain less chem energy
the enegry released in turn is used to power work of cell
first law of thermodynamics
the law of conservation of energy which states that the universe conatins a cosntant amount of enegry
enegry is neitehr created or destroyed
energy justc ahnesg from one form to anotehr
second law of thermodynamics
when we change energy forms tje total amount of energy remains constant
but change energy forms, the enegry available to do work decreases
energy transformations arent 100% efficient beacsue amount of enegry available to do work decreases every time enegry changes forms
energy not availble to do work takes on form of increase in disorder
second law states that trasnformtaion of energy is assocaited with an increase in disorder of universe
like when kinetic energy changd to potential amount of disorder increasses - degree of disorder is called entropy
entropy can also be considered the number of possible psouton and motions (microstates) a molecule can have - as entropy inc the number of poositons and motions availble also inc
in chem rxns entropy inc usually happens through tehrmal energy release which we experience as heat
thermal enegry is form of kinetic eenrgy correpsonding to motion of molecules and results in a given temp - higher temp, more rapid moevment and more disorder
catabolic rxns result in increase of entropy as single ordered moelcule is broken down into several smaller ones with more freedom to move around
anabolic rxns decrease entropy becasue they use invidual building blocks to syntehsize an ordered molecule
this doesnt viilate 2nd law becasue it applies to universe as whole - a local dec in enttropy results in higher inc in entropy of surroundings
all cells and organisms requrie constant input of enegry to maintain their high degree of organization and function - this input comes form sun or enegry stored in chem compounds
this energy allows moelcules to be built and otehr work to be carried out and leads to entropy
chem rxns
chem rxns are central to life rpocesses
a chem rxn is process by which molecules called reactants are transofmed into otehr moelcules called prodcts - atoms change shared bonds
many chem rxns are readily reversible: prodcts can react to form reactants
reversability indicated by double arrow
chemcial equillibrium
the rate of forward reaction equals rate of revrse reaction and teh conc of reactants and products dont change
diretcion of rxn can be ifnelucned by cocn of reactants and products
ex. inc teh cocn of reactants then this favours forward rxn to produce more products
this explain how many rxn in metabolic pathways proceed: products of many reactions are quickly consmyed by next rxn to drive the first rxn forward
laws of thermodynamics detrmine whetehr chm rxn requries or releses enegry
amount of enegry aviable to do work is gibbs free energy
we can compare fre enegry of reactants and products to detrmine whetehr the rxn releasds enegry thats available to do work
if products have more free energy then gibbs is pos and net input of enegry is needed to drive rxn forwrad - endergonic - not spontanous
if products have less free energy than reactants then gibbs is neg and enegry is released and available to do work - exergonic - spontanoues
total amount of enegry is equal to energy available to do work and enegry not availble to do work
- this equation is total amount of energy which is enthalpy H is equal to gibbs free enegry + enegry lost to entropy (s) mutkplied with absolute temp because temp infleuces the moveemnt of molecules and tehrefore degree of disorder
G= H -TS
equation is useful to see if chem rxn takes place spontanously and whetehr net enegry is required or released
hydrolysis of atp is exergonic
atp reacts ith water to form ADP and inogrnaic phosphate
this si hydrolysis rxn - the water moelcule is split - rxn breaks down polymers into subunit
rxn of ATP with water is exergonic beacsue less free energy in products than in reactants
phosphate groups of ATP are neg charged and repel each other - ADP is more stable beacuse one less phosphate meaning less chem energy in the bond so value of enthalpy is neg - entropy increases so pos value - therefore gibss is neg and reaction is spontanous and releases energy to do work
free energy of ATP hydrolysis is ifneluced by many factors including cocn of reactants and rpoducts, pH of solution, temp and pressure
release of free enegry during atp hydrolysis comes form breaking weaker bonds (more chem enegry) in reactants and forming mroe stable bonds (with less chem enegry ) in the products - the release fo free enegry then drives chem rxns and other processes that require net input of energy
coupling of rxns
anabolic rxns arent spontanous
energtic coupling is a process in which spontanous rxn dirves nonspontaneous rxn
it requires that the net G of two reactions be neg
the two rxn must occur together or be coupled which can only happen if the two rxns share and intermediate
ex. atp hydrolysis can drive a nonpsontanous rxn like addition of phpshate to glucose
phosphate is trasnfered which was released form hydrolysis - net G is neg
follwiing ATP hydrolysis, the cell needs to replensih its ATP so that it can carry out additional chem rxns
synthesis of ATP from aDP and Pi is endorgnic requriing inpit of enegry
exergnic rxns can drive syntehsis of ATP by enegrtic coupling sometimes
hydrolsis rxns can be ranked by free enrgy differences
adp accepts phosphate group and enegry while ATP donates phophste group and enegry
rates and enzymes
chem rxns in cell are accelrated by catalysts
rate fo chem rxn is the amount of product formed per unit of tuime
catalysst are subtances that inc the rate of chem rxns without being consumed
they afefct both forwardd and reverse rxn and dont chaneg the equillibirum state
in biologcial systems catlsyst are usually proteins called enzymes
some RNA molcules also have catalytic activty and so do metal ions
eznymes inc the rate of reaction dramatically
eznyems are highly speicifc acting only on certain reactants and catalyzigg only some rxns they play a critical role in detrming which chem rxn take place form all the possible reaction that could occur in a cell
enzymes reduce activation energy
all chem rxns require an intial input of enegry to proceed
as chem rxn proceeds existing chem bonds break and new ones form
for a brief period of time a ocmpound is formed in which the old bonds are breaking and the new ones are forming - this intermediate is called transition state and its highly unstable and has large amount of free energy
to reach the trasnition state, the reactant must absorb enegry from surronudings
all chem rxns require an input of enegry that can be thought of as barrier
the energy input necessary to reach trasnition state is activation energy
once transition state is rech rxn proceeds, prodcyts are formed and enegry is released into surrondings
theres an inverse correlatin betweenr rate of rxn and heigh of energy barrier: lower the energy barrier, the faster the rxn and higher the barrier slow the rxn
in cells enzymes accelrate chem rxns
enzymes reuce teh actviation energy by stabalizng teh trasnsition state and decreasing its free energy - as actviation energy decreases, teh speed of rxn increases
although enzyme dec the activatione negry the difference in free enegry between reactants and products doesnt change - only path changes
Enzymes forming complex
enzymes partciapte in rxn but arent consumed
enzymes form a complex with reactnats and products
reactant catalyzed is substrate
susbtaret first form complex with enzyme and its converted into rpoduct then the complex dissociates reelaisng enzyme and product
formation of enzyme substrate complex is ciritcal for accelerating rate of chem rxn
specific interctions between enzyme and subtrate in complex stablize teh transition state and decrease the actviation enegry and then the rxn proceeds more quickly
active site
to form enzyme substrate complex, enzymes bind substartes at a region of enzyme called active site
in active site, enzyme and substrate form trasnient covalent bonds, weak non covlaet interactions or both
these inetractions stablize transition state and tehrefore decrease actviation enegry
eznymes also reduce energy of activation by position two susbtarets to react: within active site their rective chem groups are alugned and motion relative to each other is restrained
enzymes are folded into 3d shaoe which brinsg particular aa into close proximity of active site
size of active site is small
many of aa that form active site, only a few contribuet to catalysis
enzymes are large becasue each of aa occupies specici spatal position to align with reactive group on substrate
enzymes are remakrly specific for the substrate and reaction being catalyzed
structure of active site only interacts with substrate that has compelemnatry structure
lock and key model is that substrate fits into active site - specific interaction - enzymes speicifc for substartes
indicued model fit - bidning of substrate to atcive site slightly modfies the shape of active site - shape of substrte might also be infleucned by bidning teh active site - fit becomes closer when they inetract - they can both mold to a certain degree
Cofactors
many enzymes require additional nonprotein moelcules called cofactors for their function
they can be inorganic or organic
inorganic can be metals while organic can be diverse and things like vitamins
metallic cofactors bind to diverse proteins including enzymes used in DNA syntehsis and nitrogen metabolism
metallic cofactors also bind to enzymes used in transport of electrons for cellular repriation and photosynthesis
enzyme kinetics
enzymes inc the rate of chem rxns and kinetics is the study of rates of reaction
Menten and Michealis proposed a model for enzyme kinetics thats refefred to as michealis menten model
simplest model of enzyme action involves chem rxn with single susbtrate, enzyme and product
as cocn of susbtarte increases the reactuin rate inc and then levels off - as substrate conc increases, they bind to enzyme until all active sites are bound - the enzyme is satruated with subtrte and reaction rate cannot inc furtehr
temp and pH on enzyme activty
as temp inc, tehre is inc in tehrmal energy which inc the motion of molecules inc interaction
actvity of enzymes is sensitive to temp
enzymes have optimal temp
at low temp enzyme atcity os low beacsue moelcules move slowly or have low kinetic enegry reducing probability of interaction
as temp inc the molecule move around more rapidly and have high kientic enegry which increaes theri chance of inetracting with one another
at rlly high temps the enzymes unfold or denature - loses ability to catalyze rxn
diff enzymes work best at diff temps
enzyme activty also infleucned by pH
enzymes have optimal pH
most are pH of 7 but some excpetions like diegstive enzymes or lysomsoic
pH can inclufe how enzyme folds - pH impacts charges of aa which affects how aa interact when folding
pH can also affect charged of aa that make up active site - charges of aa tehn ifnelucne how well it binds with substrate
activators and inhibtors
inhibtors dec the activty of enzymes while actvitors inc
enzyme inhibtors are common - can be ysntehsized normally
inhibtors can compete with usbstrate for active site of enzyme - competitive inhibtor - similar in strcyrue to substarte - you can inc the cocn of susbtaret to overcome
noncompetive inhibtor bind to site other than active site which changes the shape and activty of enzyme - doesnt charnge shape of active site or ablity of enyzme to bind substrate
allosteric enzymes
enzymes that are regulated by moleucles that bind at sites otehr than active site
activty of allosteric enzyme can be ifnleuced by inhbtors and activators
play key role in regulatin of metabolic pathways
negtaive feedback is when final product inhibts first step of rxn - usualky done to maintain homeostaiss
these caatalyze key rxns in metabolic pathways
these enzymes are found at or near the start of metabolic pathway or at crossroads between two pathwas
