biochem2 Flashcards
what is bioenergetics?
Thermodynamics of a biological system
Three students are reviewing a chart in their biochemistry text showing that many of the individual steps of glycolysis have a positive G’ value. Which student has the correct explanations for why glycolysis still occurs readily in living systems: Student A) Enzymes are the solution! Enzymes drastically lower the free energy change to be more negative. Student B) Food energy is the solution! Many biochemical reactions are unfavorable and that is why we must eat—to provide external energy to drive these reactions and maintain disequilibrium. Student C) Reaction coupling is the solution! While some reactions are unfavorable, they are coupled to reactions that are favorable.
Student C
Several steps in glycolysis have positive ΔG’s, but the pathway still occurs spontaneously in cells.
Student C is correct, reaction coupling will drive the entire pathway forward. Some steps in glycolysis have positive ΔG’s, but other steps have very negative ΔG’s. Those steps require the products of previous steps. Because the reactions are linked by the product of one reaction providing the substrates of the following reactions, the very negative ΔG’s will pull the pathway forward, even though the positive ΔG’s are earlier in the pathway than the very negative ΔG’s.
a living system require __ and ___ delta S due to all macromolecules and systems being highly ordered compared to their precursors.
large negative
What is dynamic steady state / homeostasis?
describes the ability of living things to maintain a constant steady internal environment that is NOT in equilibrium with its surrounding.
What is the difference between equilibrium and steady state?
Equilibrium is a dynamic state existing at the LOWEST possible entropy and energy for that system.
Steady state involves a constant INVESTMENT (HIGHER ENERGY) of energy for living systems to maintain a steady that is far from equilibrium.
is the human body an open or close system?
open as a whole but closed system on a cellular and molecular level.
What is delta G?
free energy change at some present, non standard set of conditions.
what is delta g knot ? DeltaG*
free energy change at standard contains of 25C, 1atm, and [1M] of all species.
what is delta G knot prime? deltaG*’
Free energy change at standard physiological conditions, pH= 7
If delta G is positive, does the equation go to the right or to the left?
to the left
If delta G is negative, does the equation go to the right or to the left?
to the right
In the equation: deltaG=deltaG’+RTlnQ
what is delta G?
what is deltaG’
R= universal gas law constant t = temperature q= reaction quotient deltaG'= fixed unchangeable deltaG= is variable and can be measured anywhere at any time during a reaction.
Students frequently hold misconceptions about G and G’. Check yourself with the following: T/F?
a) For Reaction X, G = -30.78 kJ. For Reaction Y, G = 22.5 kJ. It can be concluded that Reaction Y is closer to its equilibrium than is Reaction X,
b) At equilibrium, G’ = 0,
c) At equilibrium G = 0
d) For a given reaction at a given temperature, there are an infinite number of different G’ values associated with different ratios of products to reactants,
e) For a given reaction at a given temperature, there are an infinite number of different G values associated with different ratios of products to reactants,
f) G*’ represents the free energy change for a complete conversion of all reactants to products.
a) true 25 is closer to 0 than 30.
b) false
At equilibrium, because deltaG’ = -RTlnKeq and at equilibrium, ΔG = 0
c) true
d) false
e) true
f) false
what are parameters of an endergonic reaction?
delta G is positive = non spontaneous
what are parameter of an exergonic reaction?
deltaG is negative= spontaneous
T/F?
a) If Keq =1,G*=0
b) If Keq =1,G=0
c) If Keq =Q,G=0
d) If Keq =Q, G=0
e) If Q=1,G=0
f) If Keq =1,G=G
g) If Q=1,G=G
h) If Keq >1, G must be negative,
i) If Keq > 1, G must be negative.
looking at delta G=deltaG’+RTlnQ and deltaG’ = -RTlnKeq
a) true
b) false
c) true - If Keq = Q, the reaction is at equilibrium, and ΔG = 0.
d) false
e) false
f) false
g) true- ΔG = ΔG° + RTln(Q). Since Q = 1 and Ln(1) = 0, ΔG = ΔG°.
h) true- ΔG° = -RTlnKeq
i) false
1) The post-translational folding of the enzyme ribonuclease-A is associated with a large, negative S for the unfolded-to-folded transition. Ribonuclease-A folds spontaneously because the:
A) sum of the heats of formation of all folding interactions in the native conformation is large and negative.
B) sum of the heats of formation of all folding interactions in the unfolded conformation is large and negative.
C) change in entropy for the unfolded-to-folded transition is large and positive.
D) change in entropy for the unfolded-to-folded transition is small and positive.
a
what is ATP?
primary energy currency in human body
Delta G*’ for ATP HYDROLYSIS has to be less or more than 0?
a lot less than 0
when you lose phosphate group and go from ATP –> ADP –> AMP, is the transition end or exergonic? which is the highest energy molecule?
exergonic
cAMP is higher energy molecule than ATP.
What is the AMP-> cAMP transition; endo or exergonic?
endergonic which is why cAMP is a higher energy molecule than ATP.
What is substrate level phosphorylation?
process by which ATP is formed from ADP. Process must be bound to an exergonic reaction.
where does substrate level phosphorylation occur?
primarily in cytosol as part of glycolysis but also in matrix of mitochondria where GTP is formed during Citric acid cycle
what is oxidative phosphorylation?
formation of ATP out of ADP and free organic phosphate (Pi) by harnessing energy of proton gradient across inner mitochondrial membrane.
Proton gradient causes by oxidation of NADH and FADH2.
ex: ATP formed by the ATP synthase complex in the mitochondria
where does oxidative phosphorylation occur?
exclusively in mitochondrial matrix.
What is equation for hydrolysis of ATP?
ATP + H2O –> ADP + Pi + energy
then couple to another equation
What is equation for Phosphoryl group transfer?
ATP ADP + energy, but the phosphate is transferred onto another molecule, rather than being releases as Pi.
What is phosphorylation using ATP? what is its importance in the body?
phosphoryl group transfer
Major human body regulation mechanism where enzymes, proteins and signaling molecules are turned on/ off by phosphorylation.
ATP acts as donor of phosphate group.
In the reaction
GADP + NAD+ + Pi –> 1,3 BPG + NADH
which molecules are reduced? which are oxidized?
In the reaction, GADP is the reduced form, NAD+ is the oxidized form 1,3 BPG is the oxidized form, and NADH is the reduced form. Thus NAD+ is being reduced (it is an oxidizing agent) and GAPD is being oxidized (it is a reducing agent).
When you see NADH/NAD+, NADPH/NADP+ FADH2/FAD, FMNH2/FMN, semiquinone (an FMNH radical), ubiquinone, or cytochrome; think about what type of reactions?
REDOX
What is aerobic versus anaerobic respiration?
Respiration is a process in which an in organic compound serves as the ultimate electron acceptor in order to generate ATP.
Aerobic respiration uses oxygen as the final electron acceptor, while anaerobic respiration uses a molecule other than oxygen. For question purposes, aerobic respiration involves all the reactions involved in the citric acid cycle and electron transport.
Anaerobic respiration will typically refer to fermentation, using glycolysis in the absence of oxygen, or the lactic acid cycle in muscles. Humans use aerobic respiration to generate the vast majority of our ATP. However, we use anaerobic respiration in our muscles during exercise that results in a buildup of lactic acid. Many bacteria and yeast use anaerobic respiration, including during fermentation.
What is the difference between an obligate aerobe and a facultative aerobe? Between an obligate and a facultative anaerobe? Which one are you?
The term “obligate” implies that there is no other option, so obligate aerobes must use aerobic respiration and cannot survive without oxygen, while obligate anaerobes must use anaerobic respiration and cannot survive in the presence of oxygen. “Facultative” implies that the organism will use whichever respiration is available. So if oxygen is present, the organism will use aerobic respiration, and if oxygen is absent, the organism will use anaerobic respiration. Facultative anaerobes prefer anaerobic conditions while facultative aerobes prefer aerobic.
12.
What does glycogen phosphorylase do?
removes glucose residues from reducing ends of glycogen polymers –> glucose-1P
what does phosphoglucomutase do?
converts Glucose 1P –> Glucose 6P
in which metabolism are glycogen phosphorylase and phosphoglucomutase found?
Glycogen metabolism
what is metabolized in the muscle and kidney in fructose metabolism?
Hexokinase converts Fructose –. Fructose 6P.
what is the point of galactose metabolism ?
Galactose convertes to Glucose 1P through multiple steps that involve UDP as the coenzyme.
What is the role of phosphoglucomutase in galactose metabolism?
Convert Glucose 1P to Glucose 6P (which then goes to 2nd step of Glycolysis)
Fructose metabolism in the liver, what three things are converted to what by what?
1) Fructokinase converts Fructose to Fructose 1P
2) Fructose 1= phosphate aldolase converts Fructose 1P to Glyceraldehyde 3P and DHA-P
3) Triose phosphate isomerase converts DHA-P to Glyceraldehyde 3P (GA-3P is funneled to 5th step of glycolysis).
When is fermentation used by animals?
when there’s oxygen debt (like prolonged exercise) and in erythrocytes.
What is ethanol fermentation? what’s unique about it?
primarily used in yeast and in a few bacteria. Ethanol is produced and is the final electron acceptor.
IMPORTANT: carbon skeleton changes from pyruvate 3C to ethanol 2C and CO2
what is lactic acid fermentation?
lactate is produced and is the final electron acceptor.
what is the importance of fermentation?
regenerates NAD+ so that glycolysis can continue
what is gluconeogenesis/
reversal of glycolysis to produce glucose from pyruvate.
when are you likely to see gluconeognesis?
In Liver = fasting= need to increase blood sugar.
what are the four enzymes in glycolysis that are being replaced in gluconeogensis and by what?
Hexokinase/glucokinase –> glucose-6-phosphatase,
phosphofructokinase –> fructose-1,6-bisphosphatase,
pyruvate kinase enzymes –> PEP carboxykinase/pyruvate carboxylase.
those enzymes are all irreversible reactions and replaced phosphorylation reaction.
