Unit 2 Flashcards
do signal sequence, RNA-protein particle, preceptor, and channel work for any protein?
yes they are all generic
where are proteins sent once they are processed inside ER
golgi
how do finished proteins from ER travel to golgi
through tubes that extend from ER and grow along microtubules
what 2 things happen once proteins and lipids are inside golgi
- undergo final modifications
- sorted into compartments that correspond to certain destinations in cell
how do vesicles get to their destination
exterior of each vesicle membrane has proteins that act like zip codes
motor proteins like kinesin walk along microtubule
what does the endomembrane system consist of
ER, golgi, secretory vesicle, endosome, lysosome
function of ER
protein folding and modifications
function of golgi
further modifications and sorted into compartments
function of secretory vesicle
motor proteins direct vesicle to destination, soluble proteins released
function of endosome
destination, materials brought in by endocytosis and released by exocytosis
function of lysosome
path of newly synthesized digestive enzymes, site of degradation
how do proteins get to their correct cellular location
3 mechs:
1. transport through nuclear pores
2. transport across membranes
3. transport by vesicles
what are signal sequences
short sequences of amino acids that direct proteins to locations
each location is targeted with a ____ signal sequence
specific
does constitutive secretion occur continuously
yes
how are integral membranes inserted into ER membrane
co-translational translocation
describe the process for co-translational translocation
SRP pauses translation, SRP binds to receptor and translation resumes, ribosome binds to translocator, plug moves, signal sequence binds to translocator, translocation continues and protein is translocated into lumen of ER where signal sequence is cleaved, signal sequence degrades and plug closes translocator
hydropathy
amount of free energy required to move sequence of amino acids from nonpolar solvent to water
ATP has extremely ___ potential energy
high
endergonic rxn is ___
nonspontaneous, increase in free energy
exergonic is ____
decrease in free energy, spontaneous
what affect does spatial orientation have on enzymes
makes it unlikely for reactants to bump into each other at random
where do reactants move around
cytosol or interior of organelle
what is activation energy
as old bonds break and before new bonds form, there is transition state where reacting substances are much less stable than before rxn started
if the reaction is less stable, what happens to free energy
it spikes
do enzymes change free energy of reactants or products
no
what is unique about enzymes
each enzyme catalyzes one particular rxn bc size, shape, and chem composition of active site is so that reactants fit into space and bind to R-groups
what is the most accurate velocity when looking at rate of rxn
initial velocity of enzyme-substrate rxn bc rxn rate will decrease as substrate is made into product
why does plateau occur
bc enzyme is saturated so all available enzyme molecules are processing substrates
what is the rate of rxn limited by
concentration of enzyme
what is Vmax
max rate of rxn of particular enzyme at particular concentration, occurs when enzyme is saturated
what does it mean when an enzyme is saturated
all active sites are occupied by substrates
what is Km
substrate concentration that gives a rate that is halfway to Vmax, helps measure how quickly rxn rate increases with substrate concentration, measures enzyme affinity for binding to its substrate
lower Km = ____ affinity
higher
what is Kcat
turnover number, (Vmax)/[enzyme]
an enzyme that has a high efficiency would have what kind of values for Km and Kcat
low Km and high Kcat
Michaelis-Menten kinetics equation
E + S –> [ES] –> E + P
V = (Vmax x [S])/(Km + [S])
what is steady-state assumption
concentration of enzyme-substrate complex is constant over time
[ES] = constant
what is initial-velocity assumption
initial rate of rxn is measured so concentration of substrate is much higher than concentration of product
what is single-substrate assumption
assumes that enzyme-catalyzed rxn involves single substrate interacting w enzyme to form ES complex
what is reversibility assumption
reverse rxn of substrate dissociating from ES complex to form enzyme and substrate again is negligible under typical conditions
what is substrate concentration
[S]»[E] so that [S] is constant when measuring instantaneous velocity
what is an activator
molecules that increase activity of enzyme
what is an inhibitor
molecules that decrease activity of enzyme
what is noncompetitive inhibition
inhibitor and substrate can both be bound at same time
what happens to Vmax and Km in presence of competitive inhibitor
Vmax is unchanged, Km is higher
what happens to Vmax and Km in presence of noncompetitive inhibitor
Vmax is decreased, Km is unchanged
what type of rxn drives ATP production
redox rxn
what is electrical energy
flow of currents/flow of charge, used to drive molecular motors that use mech energy to product ATP
list the major steps in cellular respiration
glycolysis, pyruvate processing, citric acid cycle, e- transport chain, ATP synthase
how many ATP does glycolysis produce
2
what reactant does glycolysis begin with
glucose
what does glycolysis end with
2 pyruvate
where does pyruvate processing happen
single multi-unit enzyme complex
what does pyruvate start with as a reactant
pyruvate
what does pyruvate processing produce
acetyl coenzyme A, oxidized 2 of carbons in glucose to CO2
what does citric acid cycle begin with
acetyl-CoA
how much ATP does citric acid cycle produce
2
ETC uses ___ and yields ___ as product
oxygen; water
what does ATP synthase convert ADP and inorganic phosphate into
ATP
what is oxidative phosphorylation
ATP production at end of cellular respiration
what are the 2 e- carriers
NADH and FADH2
what organelle does cellular respiration involve
mitochondrion
ETC is collection of multiple proteins embedded in ___ mitochondrial membrane
inner
in complex I, what happens to NADH
it becomes NAD+
in complex II, what happens to FADH2
it becomes FAD
what is the final e- acceptor in ETC
oxygen
if one part of the assembly line stops, what happens to ETC
e- can’t move to next position, energy stops getting released, no more proton pumping can happen
ATP synthase is complex V and the flow of current is carried by protons to a ___ that spins turbine that produces ATP
rotor
where do protons enter complex V
F0 subunit, making ATP synthase spin
what does the twisting force in ATP synthase do
causes F1 subunit to change shape to catalyze addition of phosphate group to ADP, forming ATP
which is more efficient: fermentation or cellular respiration
cellular respiration
how does fermentation work
pathway that transfers e- from NADH to carbon-based molecule to regenerate NAD+ and keep glycolysis running to produce small amounts of ATP
diff between anaerobic and aerobic respiration
anaerobic: e- reduce substances other than oygen (SO42-, CO2, NO3-, NO2-)
aerobic: oxygen acts as final e- acceptor in ETC
catabolic pathways ___ molecules
break down
anabolic pathways ____ molecules
build and create
allosteric regulation
regulatory molecule (activator or inhibitor) binds to enzyme someplace other than active site
what is the site called when regulatory molecule binds to enzyme someplace other than active site
allosteric site
almost all cases of noncompetitive inhibition are forms of _____ regulation
allosteric
allosteric activation
activation of enzyme’s activity by molecule binding to allosteric site
allosteric enzymes
have multiple active sites located on diff protein subunits
cooperativity
substrate itself can serve as allosteric activator, when it binds to one active site the activity of other active sites increase
cofactors
non-protein helper molecules that can attach temporarily to enzymes through ionic or hydrogen bonds or permanently through stronger covalent bonds
many enzymes don’t work optimally or at all unless bound to ___
cofactor (ex. Fe2+, Mg2+)
coenzymes
subset of cofactors that are organic molecules (Vitamin C)
what does compartmentalization enable
segregation of enzymes involved in diff metabolic pathways, regulating cellular processes
feedback inhibition
end product of metabolic pathway acts on key enzyme regulating entry to that pathway so that it keeps more of end product from being produced
can the cell turn off its own pathway to ensure it makes the right amount of product
yes
what happens if there’s little product
enzyme won’t be inhibited and pathway will continue to replenish
what happens if there’s lots of product
cell will block enzyme and prevent production of new product until existing supply is used up
what catalyzes pathway steps regulated by feedback inhibition
allosteric enzymes
what happens to cellular respiration when oxygen is depleted
O2 cannot accept e- at end of ETC, e- build up in ETC and e- can’t enter, NADH and FADH2 build up so NAD+ isn’t available for glycolysis
fermentation allows cells to regenerate ___
NAD+
what is reduced and oxidized in fermentation
pyruvate is reduced, NADH is oxidized
what is produced for 1 glucose molecule
2 ATP, 2 lactate, 2 NAD+ generated
what is metabolic flux
movement of metabolite through pathway over time
reversible rxns have change in free energy close to ___
zero
irreversible rxns have change in free energy ___ zero
less than
true or false: metabolic pathways never come to equilibrium bc free energy is required to do work
true
what is the equation for photosynthesis
CO2 + H2O + light energy –> carbohydrate + O2
what is oxidized in photosynthesis
oxygen
what is reduced during photosynthesis
carbon atom
what is first stage in photosynthesis
energy in specific wavelengths of light is absorbed by pigments which causes e- to be excited in high-energy state
what happens in PSII
excited e- are passed to molecule called PQ (reducing it), transforms light energy to chem energy
what does PQ do once excited e- are passed to it
carries e- out of PSII and passes it to ETC to pump protons across membrane
describe stage 2 of photosynthesis
pigment molecules in PSI, excited e- passed through series of carriers until they reach enzyme that uses energy to catalyze reduction of NADP+, completes transformation of light energy captured in PSI to chem energy
NADPH is e- carrier and reduced form of NADP+
what happens in stage 3 of photosynthesis
ATP and NADPH produced from energy kept in PSII and PSI are used in Calvin cycle that results in reduction of CO2 to produce sugars
where are PSII, ATP synthase, PSI found
chloroplasts, membranes of flattened sacs so there is high proton concentration
what does the Calvin cycle begin with
CO2 added to 5-carbon sugar
what does Calvin cycle produce
glucose
what is rubisco
enzyme that catalyzes first step in calvin cycle
how does rubisco work
attaches to CO2 molecule to 5-carbon sugar that is regenerated at end of each turn in cycle
what does rubisco produce
2 identical molecules of 3-carbon sugar
what does rubisco catalyze the reduction of
CO2
true or false: rubisco is most abundant enzyme on earth
true
what happens when CO2 levels in chloroplast are low
O2 can bind to active sites and be added to 5-carbon sugar that acts as substrate
how does CO2 get to chloroplasts
plant stems covered with wax blocks movement of water away from plant and keeps stems and leaves from drying out; stems and leaves have openings called stomata in epidermis that aren’t covered in wax where CO2 can diffuse in and O2 diffuse out
what regulates size of stomata
specialized guard cells
where does plant mass come from
CO2 in air
