Unit 2 Flashcards
what does work do
work creates order. it lowers the entropy of the system
energy is always
converted when work is done. energy is degraded as heat in any reaction when work is done so it lowers the work potential
second law of thermodynamics
entropy is continuously increasing and energy transformations proceed spontaneously to convert matter from more/less stable to more/less stable forms.
positive Gibbs free energy
products have more free energy than reactants. this is endergonic
negative Gibbs free energy
products have lower free energy than reactants. this is spontaneous and exergonic
endergonic
this is anabolic (stores energy) and may not occur even when enzyme is present because the activation energy is so high
exergonic
is catabolic (releases energy) and may occur spontaneously. the negative delta g can be used to do work
metabolism
sum of catabolic and anabolic reactions
coupling
to accomplish anabolic reactions, you can pair them with an exergonic reaction such that the net delta g is negative
combustion vs aerobic respiration
different as the bonds are not broken by heat in combustion. it also is a generalized reaction, there are mayn intermediate steps.
why can’t you break down glucose all at once
beause then all the energy would release at once and when that happens, a lot of heat is released
oxidation
looses electrons and energy. can also transfer protins (H+)
reduction
gains electrons and energy
glycolysis takes place in
the cytoplasm
cleavage why
it becomes an acid here (before it was a sugar). it was also really unstable so it splits
substrate level phosphorylation
occurs in glycolysis times 2. yields 4 atp.
substrate level phosphorylation process
ATP is formed by transferring a phosphate group directly to ADP from an intermediate. during glycolysis, chemical bonds are shifted around to provide energy required to form ATP.
reduction of NAD+
(endergonic maybe) carries electrons around to donate hydrogen to other molecules
net yield of glycolysis
2 ATP, 2 NADH + H+, 2 pyruvate
glycolysis is limited by
glucose supply and availability of oxidized NAD+ carriers
What is NAD+
enzymes use NAD+ as a cofactor for oxidation reactions.
energy stored in NADH vs ATP
ATP: you can release it suddenly. it can’t be stored
NADH: this can store potential energy for longer periods of time than ATP
how does ATP drive an endergonic reaction?
enzymes that catalyze reactions have two binding sites: one for reactant and one for ATP. the ATP site splits the ATP molecule which releases energy allowing the endergonic reaction to occur.
ATP synthesis is a ___ reaction
endergonic reaction which requires energy from cellular exergonic reactions
oxidative phosphorylation
ATP is synthesized by ATP synthase using energy from a proton gradient. this gradient is formed by high-energy electrons from the oxidation of glucose passing down an electron transport chain. These electrons, with their energy depleted, are then donated to oxygen, hence the term oxidative phosphorylation
why don’t cells just link the oxidation of glucose directly to cellular functions that require the energy
would be inefficient
recycling NAD+
as long as there are food molecules, cell can churn out ATP but it accumulates NADH and depletes the pool of NAD+. A cell does not contain a lot of NAD+so it must recycle it
1) aerobic respiration
2) fermentation
pyruvate after glycolysis
aerobic conditions: pyruvate is further oxidized to yield ATP
anaerobic: pyruvate is converted to lactic acid
from cytoplasm to the mitochondrial matrix
the 2NADH+H+ gets oxidized by a protein. the electrons get transferred to FAD (turns to 2FADH2). pyruvate also crosses the membrane. this process requires two ATP which is why there are usually 38 ATP in prokaryotic cells since they don’t have membranes to cross
glycolysis reactions summary
1) priming reactions use up two ATP to reduce activation energy
2) cleavage occurs and there are 2 G3P (3 carbon phosphates)
3) oxidation and ATP formation NAD+ gets reduced (x2) to add in another phoshate. ATP is formed using substrate level phosphorylation (x2x2) as phosphates are removed
Krebs cycle takes place in
the mitochondrial matrix
how many electrons does it take to reduce NAD+?
two electrons
pyruvate oxidation
link reaction that results in pyruvate being oxidatively dehydrogenated by an enzyme.
1) oxidation of pyruvate produces reduced NAD+ to NADH + H+
2) decarboxylation which produces CO2
3) addition of remaining Acetyl group to coenzyme A through condensation synthesis.
after pyruvate oxidation, what happens
pyruvate + NAD+ + coA turns to Acetyl-coA and NADH+H+ + CO2
krebs cycle steps
1) condensation: addition of acetyl group through coenzyme A. adds to 4 carbon group and becomes a 6 carbon.
2) first oxidation: oxidation and decarboxylation of the 6 carbon then produces reduced NADH + H+ and carbon dioxide which turning it into a 5 carbon
3) second oxidation: 5 carbon becomes 4 carbon through this process again
4) substrate-level phosphorylation: adding in another coA is a high energy bond. bond is cleaved and the energy is used to produce ATP. still a 4 carbon
5) third oxidation: FAD gets reduced here to FADH2 since the bonds are lower in NADHenergy between this 4 carbon molecule. still stays as 4 carbon
6) regeneration of oxaloacetate: NAD+ gets reduced and 4 carbon original returns
Krebs cycle totals
2 pyruvate turns to: 8NADH + H+ + 2FADH2 + 2ATP
2 NADH + H+: 2FADH2
Electron Transport chain
1) NADH Dehydrogenase: 8NADH+H+ oxidizes to 8NAD+ and drops of 16 electrons which is used to pump an H+
2) 4FADH2 drops off 8 electrons and becomes 4FAD through oxidation
3) electrons move to bc1 complex (through cytochrome c) and it pumps out another H+
4) cytochrome oxidase complex: uses 24 protons (16 and 8) to reduce oxygen into water.
5) the H+s are stored inside the christae of the intermembrane space, they are looking for a way out since the cytoplasm doesn’t have a equilibrium
5) ATP synthase: can be located anywhere in the membrane. due to the above steps, a chemical gradient is created. the outside of the inner mitochondrial membrane is positive due to the H+ ions and the inside is -ve due to the loss of the protons. protons are pushed through the ATP synthase protein which causes the rotor to spin and make ATP by binding together ADP and P.
ETC Totals
8NAD+ + 4FAD + 12 H2O +26-32 ATP from oxidative phosphorylation
why is it 26-32 ATP
the proton gradient is sometimes not always the same and the process can also be ineffiecient sometimes. Each person’s body is different
why regulate cellular respiration?
ATP can’t be stored for long periods of time
metabolic pathway
every step is catabolized by enzymes in a chain reaction
enzymes that are regulated
phosphofructokinase and pyruvate dehydrogenase
phosphofructokinase
(Noncompetitive- binds to allosteric site)
ACTIVATE: ADP allows more efficient binding of substrate therefore more glucose production
INHIBIT: ATP binds to the allosteric site using energy which means less breakdown and less ATP produced
- high levels of citrate can also inhibit this enzyme
pyruvate dehydrogenase
main commitment step in krebs cycle is converting pyruvate to acetyl-coA using dehydrogenase
INHIBIT: high levels of NADH from Krebs cycle competitively binds to this enzyme which stops the exchange of electrons of pyruvate to Acetyl coA. also Acetyl-Coa and ATP
ACTIVATE: NAD+, ADP, Pyruvate
what is made when energy stores are low?
acetyl-coA
what happens when body has less oxygen
- cause buildup of electrons in ETC due to little oxygen being diminished
- no movement in ETC would mean no oxidized electron carriers (NADH or FADH2) so krebs cycle stops as well as pyruvate oxidation
aerobic respiration
needs oxygen, occurs in most cells, makes a lot of ATP, products: CO2, H20 and ATP, occurs in cytoplasm and mitochondria, Reactants: glucose, oxygen, complete combusion
anerobic respiration
without oxygen. some organisms have evolved to use other atoms to accept e- for cellular respiration
- the free energy is less since oxygen is more electronegative than other elements
- other atoms have higher bond energy than oxygen does so less energy is released in reaction
what do most organisms due in anaerobic respiration conditions
fermentation. the purpose is to use organic molecules to accept the electrons from glycolysis in order to recycle the oxidized NAD+ that is required for process to continue.
Organic molecule + NADH –> reduced organic molecule + NAD+
fermentation
in low oxygen conditions, glycolysis still continues while krebs and etc shut down
there are two types
alcohol fermentation
- yeast does this
1) glucose goes through glycolysis
2) pyruvate gets decarboxylated (yields CO2) and turns to acetyl aldehyde which turns to ethanol after accepting a pair of electrons from NADH
3) this produces NAD+
lactic acid fermentation
- most animals cells do this
1) glucose goes through glycolysis
2) pyruvate turns to lactic acid after accepting a pair of electrons from NADH
3) this produces NAD+
Ethanol and lactic acid toxicity
Ethanol: super toxic for yeast
lactic acid: less toxic than alcohol. decreases the pH which denatures enzymes. liver can convert this lactic acid back to glucose later but it takes ATP to break down lactic acid which is why it is called “oxygen debt”
energy systems and exercise
depending on type and duration of exercise, different energy systems produce ATP
creatine phosphate system
anaerobic
- creatine is made from 3 amino acids
- made in liver and then urinated out
- allows muslce cells to have 15 sec of energy
- stored in skeletal muscles. heart and brain
creatine phosphate system process
- bond between creatine and phosphate splits and energy is liberated, through hydrolysis of phosphate bond, the phosphate moves (through substrate level phosphorylation) from creatine to ADP to ATP immediately
- can be stored longer than ATP since its more stable
glcolytic or lactic acid system
anaerobic
- basically the lactic acid cycle
- supplements moderate to high intensity activity for up to 45 sec or can supplement aerobic ATP generation over long periods of time if exercise levels exceed the areobic capacity but are below maximum
- other sugars can be fed into glycolysis from food
- see gluconeogenesis
gluconeogenesis
when glycotic metabolism exceeds oxidative phosphorylation, glycolysis’ end product, lactace gets returned to liver. it requires ATP to reproduce glucose from lactic acid which occurs in cori or lactic acid cycle
oxidative system
can use many macromolecules to make energy during more moderate activity for long duration
- nucleic acids, proteins, polysaccarides and lipids
nucleic acids
break down to nucleotides which feed into Krebs cycle which produces H2O and CO2
proteins
anaerobic deamination
- break down into amino acids
- remove the amino group from each acid a
- deaminated amino acid moves to Kreb’s cycle as 5 carbon acid or as 3 carbon acid like pyruvate in pyruvate oxidation link reaction
turns into NH3, H20 and CO2 as waste
polysaccarides
anaerobic
- broken down to sugars then into glycolysis and cellular respiration which turns into H2O, CO2 waste
lipids and fats
aerobic beta-oxidation
- fats are broken down into fatty acids plus glycerol
- enzymes remove the 2 carbon acetyl group over and over until the full acid is converted to acetyl groups
- each acetyl group is then combined with Coenzyme-A to oxidatively form acetyl-coA this goes into the krebs cycle and is oxygen dependent which explains why aerobic exercise burns fat but anerobic does not
H20 and CO2 waste
ATP produced per catabolism of fatty acids
x carbon fat
x/2 ATP
3x NADH= this is ATP from oxidative phosphorylation
x FADH2= this is ATP from FADH2
12 carbon 6 ATP 18 NADH = 54 ATP 12 ATP from FADH2 TOTAL: 72 ATP
fats vs carbohydrates energy
fats have 20% more energy than glucose. 1g of fatty acid contains 2x as much energy than 1g of glucose. fats are not metabolized since they take a long time
fats require more oxidation to break down than carbohydrates, thus yielding more energy but at a slower rate.
bar graph vs scatter plot
bar graph is comparing things and numerical values (ie dormant vs germinated respiration) while scatter plot is one thing measured over a range of other numerical values (i.e temperature and rate)
CO2 and rate of respiration
More waste product means higher “rate of reaction” and more glycolysis occurring.
germination and rate of respiration
germinated have higher CO2 since they require a lot of ATP to access the nutrient stored in the endosperm and kick-start the initial root and stem growth
dormant require barely any CO2 as they are not growing and don’t require as many nutrients and ATP as germinating seeds.
temperature and rate of respiration
At lower temperatures, both the kinetic energy of the molecules is lower and the seed also wants to produce ATP at a slower rate. The enzymes that catalyze cellular respiration won’t work as efficiently as they are significantly below their optimum range. This allows the seed to conserve its energy, which is a simulation of what would occur during winter.
the higher the temperature, the higher the rate of reaction. This is because the kinetic energy of the system allows the reaction rate to increase as the molecules collide with each other so much more frequently. Also, the enzymes that catalyze the reactions of respiration have an ideal temperature at which they perform.
During aerobic respiration oxygen gas is consumed at the same rate as carbon dioxide gas is produced. In order to provide accurate measurements of oxygen consumption, what should the experimenter ensure that they do? (2A)
Include a device that removes CO2 from the volume of the container
why would an organism have higher CO2 rate at lower/higher temperatures than in other places
they have to maintain both inner body temperature and do cellular respiration so more ATP
in a lab
mention
- equipment used
- removal or waste products that you are not measuring
- include a control with nothing in it
- controlled variables
- independent and dependent variables
- repeat a few times for accuracy
pH and co2
an optimum range for the enzymes in cellular respiration and outside of that range it would denature the enzyme and lower the rate anything to that effect would be acceptable.
ATP yield totals
Glycolysis: 2 ATP, 2NADH turns to 6 ATP so 8 ATP
oxidation of pyruvate: *2NADH turns to 6 ATP
Krebs: 2 ATP, 6NADH turns to 18 ATP and 2FADH2 turns to 4 ATP
TOTAL: 38 net ATP
* In eukaryotes, 4 ATP is produced here
if the ability of cellular respiration is diminished
a cell would need to metabolize more fuel to achieve the typical ATP yield, in essence, raising the cells metabolism, storing less carbohydrates and fats, which potentially results in weight loss.
feedback inhibition:
cell produces more quantity of product through a biochemical pathway, the buildup of that product will inhibit the activity of that product’s production
when pH changes a little (product and substrate)
there is less product produced and more denatured enzymes so the rate of disappearance of the substrate is decreased!
a process common to all living prokaryotes and eukaryotes, aerobic and anaerobic is
glycolysis
a single glucose molecule can drive the Krebs cycle
2 turns
NADH and FADH2 are
coenzymes
FADH and NADH comparison:
FADH is lower in energy since it can only pump 2 H+ vs NADh which can pump 3
which one is organic, coenzymes or cofactors?
coenzymes
which one is inorganic, coenzymes or cofactors?
cofactors
in an anabolic reaction,equilibrium will favour
reactants over products
free energy
what remains after the amount of energy due to the degree of disorder of the system is subtracted from the difference between the bond energy of the reactants and products
second law of thermodynamics (mutiple choice thingy)
order spontaneously goes to disorder
*spontaneously does not mean quickly
location of the ATP synthase protein
inner membrane
Krebs cycle location
matrix
Formation of pyruvate location
cytoplasm of cell
electron transport location
inner membrane
Lowest pH location
intermembrane space. This is due to the electron transport chain and the large concentration of H+ ions
pyruvate oxidation location
matrix
many of the proteins in the ETC ARE ____ which incorporate an iron atom in haeme prosthetic group
cytochromes
anaerobic
without oxygen. uses a respiratory transport chain but does not use oxygen as the electron acceptors, mostly in prokaryotes, less ATP, Products: CO2, reduced species, ATP, occurs in cytoplasm and mitochondria, Reactants: glucose, electron acceptor (not oxygen), incomplete combustion and produces either ethanol or lactic acid
what would happen to muscles under prolonged anaerobic conditions?
lactic acid fermentation
38 vs 36 ATP
38: Prokaryotes make 2 more ATP as, in the pyruvate oxidation stage, it takes two ATP to transfer across the membrane therefore 36 net ATP
H
total energy of the system
TS
absolute temperature times the degree of disorder. represents the degraded energy
catabolic example
releases energy so respiration and digestion
anabolic example
protein synthesis and photosynthesis
in a redox reaction, electrons move from a ___ energy state to a ___ energy state.
higher, lower. this is because electrons are at a higher energy level when they are associated with less electronegative atoms (such as C or H) and at a lower energy level when they are associated with a more electronegative atom (such as O)
H+ gradient and chemiosmosis
H+ stored in intermembrane space have a force called ‘proton motive force’ since they have both high concentration and high charge and their movement can be a form of “potential energy”. They find ATP synthase which allows the protons to move and create ATP
cash
exchange goods and services, draw out of bank, ATP
investments
longer form of energy storage, lipids
checking account
glucose
saving account
longer period, used to top up checking glycogen
why can’t energy be stored in NADH or FADH2
they are large expensive molecules to make so it can’t be stored for long
how does coupling help in cellular respiration
oxidation of glucose releases free energy which can be used as the activation energy for reducing ADP.
coupling reaction example
sodium potassium pump: It’s energetically unfavorable to move sodium (Na+ ) out of, or potassium (K+) into, a typical cell, because this movement is against the concentration gradients of the ions. ATP provides energy for the transport of sodium and potassium by way of a membrane-embedded protein called the sodium-potassium pump (Na+/K+ pump).
how to draw a reaction graph
y: free energy of system
x: reaction progress
noncompetitive inhibition
binds to the allosteric site on enzyme (not denatured, only temporarily changed)
