test 1 ch 3 Flashcards
What is the point of bioenergetics?
Cells are highly organized systems
The laws of thermodynamics explain why energy is
needed to create order in cells
Understanding energy from this perspective sets up
discussion of energy flow in biological systems,
including cell respiration and photosynthesis
first law of thermodynamics states that
- Energy cannot be created or destroyed, can only be transformed into different forms of energy
-Physical World: potential to kinetic to electrical
-Biological World: light energy(photosynthesis) to bond energy (glucose) to bond
energy (ATP) and heat
-Energy used to do work
second law of thermodynamics states that
Entropy of the universe is always
increasing
- Entropy is the tendency to disorder
- Every energy transformation results in increase in entropy.
- Energy transformations not 100% efficient. Some energy lost as heat.
-Biological example in photosynthesis
-Glucose is much more ordered than CO2 and H2O from which it is made.
-Energy (in the form of light) must be added and heat is released. Release of heat causes more disorder (increased thermal motion) in the environment.
How do cells create order in a cell?
Convert forms of energy into energy in
chemical bonds
All chemical reactions must:
-Obey laws of thermodynamics
-Result in more disorder
- No energy created or destroyed
Energetically favorable reactions result in loss in free energy, deltaG
energetically favorable reactions happen
spontaneously. These are reactions that release energy when they happen.
Because energy is released, nature loves these reactions—they just go without needing extra help.
Why are they spontaneous?
Nature prefers low-energy, stable states. If a reaction moves things toward a more stable, lower-energy state, it will happen on its own (spontaneous).
creating bonds requires
energy
standard free energy: deltaG
Intrinsic energy of a reaction
Measured at “standard” conditions
- all molecules=1 M, 25o C, pH 7.0
Negative deltaG means products of reaction have lower energy than reactants (will move to the right)
Negative deltaG means that under “standard” conditions, the reaction is thermodynamically
favorable
deltaG is
represents the amount of energy available to do work in a biological system.
free energy change
Change in free energy under non-standard conditions (e.g. in a cell)
it Depends on deltaG and concentration of products and
reactants
Negative deltaG means reaction is spontaneous at a
given condition
G= deltaG+ RT ln [products]/[reactants]
- R=gas constant, T=absolute temp
-RT at 37o C = 2.58
- Units = kJ/mole
with A and B what happens as you make more product?
As you make more product, B gets bigger and as B gets bigger it’s going to be more favorable to go back the other way.
Calculation of free energy change problem
do the problem
chemical equilibrium constant:K
Chemical equilibrium is reached
when the concentration effect just
balances the push by Go.
When the ratio of
[products]/[reactants]=K, there is
no longer any net change in the
reaction
deltaG= -5.94 log K
K=10 -deltaGº/5.94 (no units)
equilibrium
the point where push from -deltaG in one direction= the push from deltaG in the other direction
chemical equilibrium problem
do it
enzymes do what?
They lower the activation energy
enzyme function
they catalyze reactions
explain enzymes
-Usually proteins (name ends in –ase or –zyme)
-Lower the activation barrier so that an energetically favorable reaction can proceed (speeds up reaction)
-Enzymes do NOT make energetically unfavorable reactions occur.
Enzymes do NOT change deltaG or K
Enzymes do not change ΔG or K for a reaction itself. However, by speeding up reactions, they can shift the balance between reactants and products more quickly. In some cases, enzymes participate in coupled reactions, indirectly influencing the ΔG of a larger process.”
what are enzyme kinetics?
Used to measure how tightly an enzyme binds to a
substrate
To measure follow the rate of product formation (or
substrate consumption)
In lab activity:
- Enzyme: Alkaline Phosphatase
-Substrate: p-nitrophenol-phosphate (clear)
-Product: p-nitrophenol (yellow)
- Measure product formation by using a spectrophotometer to
measure amount of yellow product formed
Vmax
-is when the enzyme is working at maximal efficiency (it is the max velocity an enzyme can reach)
-Units are in velocity, change in product (or
substrate) concentration per minute (e.g. mM/min)
-The only way to increase Vmax for a particular
enzyme is to increase the amount of enzyme present (concentration).
Km
is the Michaelis constant defined as the concentration of substrate at which the enzyme is working at ½ Vmax
-Units are in concentration (e.g. mM)
-Lower Km means the enzyme binds the substrate at a lower concentration and is thus
more efficient.
Use Ek to identify type of inhibitor: competitive or noncompetitive
Competitive: Vmax does not change
Non-competitive: Km does not change
do a practice problem
Driving unfavorable reactions
Energetically unfavorable reactions occur in the cell by being coupled to an energetically favorable reaction.
Coupled Reactions
A + B⟶ C +5 kJ/mole
D + C ⟶ E -13 kJ/mole
-8 kJ/mole
- Have net negative deltaG
- A product of one reaction must be used as a reactant in the
other reaction. (“C” is used as a product in the first reaction and a reactant in the second one
Activated carriers
-Energetically unfavorable reaction coupled to
-Hydrolysis of ATP or Acetyl CoA
-Oxidation of NADH or NADPH
look at model for how activated carriers work
look at model
Activated carriers are high energy molecules. What do they do?
Supply energy for biological work
Some have “high energy bonds”; breaking of these bonds has high negative deltaG, for example ATP
Some involve oxidation/reduction reactions, reduced form has “high energy”, oxidation releases
energy, for example NADH
oxidation
Removal of
electrons often by
loss of hydrogen
reduction
Addition of
electrons, often by
addition of
hydrogen
How are NADH and NADPH high energy molecules?
NAD+ or NADP+ is
reduced to NADH or
NADPH, which
carries high energy
electrons
Oxidation of high
energy electrons has
a high - deltaG
what’s an example of redox reaction as a high energy carrier
Final step in
cholesterol
biosynthesis
cells require what to create order?
energy
reactions can occur spontaneously if change in free energy is
negative
when a reaction hits chemical equilibrium what happens?
It will no longer proceed forward or backward
what do enzymes do?
Lower the barrier for an energetically favorable reaction to begin
energetically unfavorable reactions can occur if:
coupled to an energetically favorable reaction
what are activated carriers?
high energy molecules frequently coupled to energetically unfavorable reactions
Determine whether the following statement is true or false: Energetically unfavorable reactions can occur if they are coupled to a second reaction with a negative ΔG so large that the net ΔG of the entire process is negative.
true
When NADH or NADPH transfers electrons to a recipient molecule, the recipient becomes reduced and the activated carriers are oxidized (to NAD+ or NADP+, respectively). What else happens during this reaction?
Choose one:
A. A proton is released into the solution.
B. A molecule of water is released into the solution.
C. A proton is taken up by the recipient molecule.
D. A proton is taken up by the carrier.
E. A phosphate group is transferred to the recipient molecule.
C. A proton is taken up by the recipient molecule
Which statement about enzymes is not true?
Choose one:
A. An enzyme can force an energetically unfavorable reaction to take place inside the cell.
B. Enzymes reduce the activation energy required to initiate a spontaneous reaction.
C. Enzymes can help build large polymers.
D. Enzymes can speed up energetically favorable reactions.
A. An enzyme can force an energetically unfavorable reaction to take place in a cell.
Enzymes by themselves cannot make an energetically unfavorable—that is, a nonspontaneous reaction—take place in the cell. Yet, many processes that occur in cells are nonspontaneous, including anabolic pathways. How is this accomplished? It is accomplished through coupled reactions, where an unfavorable reaction is coupled to a second, highly favorable reaction, such as the hydrolysis of ATP. An example of coupled reactions is shown below, where ATP hydrolysis is coupled to drive the otherwise unfavorable reaction of glucose and fructose to form sucrose
Which of the following represents energy in its most disordered form?
Choose one:
A. kinetic energy of a moving object
B. potential energy
C. chemical bond energy
D. electromagnetic (light) energy
E. heat energy
E. heat energy
Heat is energy in its most disordered form. In contrast to the highly ordered state of a chemical bond, heat energy is the random jostling of molecules and is therefore not organized at all. As cells perform the chemical reactions that generate order within, some energy is inevitably lost in the form of heat. Because the cell is not an isolated system, the heat energy produced by the cell is quickly dispersed into the cell’s surroundings where it increases the intensity of the thermal motions of nearby molecules. This increases the entropy of the cell’s environment and keeps the cell from violating the second law of thermodynamics.
For a biochemical reaction______
energy is the term for the extra energy boost required to initiate an energetically favorable reaction within the cell.
activation
in catabolism
there is spontaneous reactions
in anabolism there are
nonspontaneous reactions
What is the difference between NAD+ and NADH?
Choose one:
NADH is an electron acceptor, whereas NAD+ is an electron donor.
NADH carries an extra proton and two high-energy electrons.
NADH is involved in biosynthetic reactions.
NADH carries an extra phosphate group.
NADH is the oxidized form, while NAD+ is the reduced form.
NADH carries an extra proton and two high-energy electrons
Which of the following does not occur in cells?
Choose one:
A. the use of heat to burn foodstuffs and transport glucose
B. the use of chemical energy to transport organelles through the cytosol
C. the metabolism of nutrients to produce useful energy stores
D. the conversion of sunlight into energy stored in chemical bonds during photosynthesis
A. the use of heat to burn foodstuffs and transport glucose
Cells do not use heat to burn foodstuffs; they use a series of catabolic reactions that allow them to break down foods and capture some of this chemical energy to power other activities in the cell. Some of this chemical energy is lost as heat. Normal cellular activities include the use of chemical energy to transport organelles through the cytosol, the conversion of sunlight into energy stored in chemical bonds during photosynthesis, and the metabolism of nutrients to produce useful energy stores.
A reaction occurs spontaneously only if the change in free energy (ΔG) is
negative
Your company has developed an organic molecule with commercial potential and you know how to produce it in the lab. You want to increase production and make as much of the molecule as possible, but the reaction has a positive ΔG°. What can you do to try to drive the reaction toward your desired product?
Choose one or more:
A. continually remove products
B. increase the concentration of reactants
C. add some products initially to get the reaction primed
D. add an enzyme that does not couple to another reaction
A. continually remove products
B. increase the concentration of reactants
Unlike ΔG°, which is a constant and is calculated when concentrations of all products and reactions are at 1 molar, ΔG depends on actual concentrations.
ΔG = free energy(products) – free energy(reactants)
Either decreasing products and/or increasing reactants will drive the ΔG to more negative values.
Chemical reactions proceed spontaneously only in which direction?
Choose one:
A. one that leads to a release of free energy
B. one that releases water
C. one that is energetically unfavorable
D. one that goes “uphill”
E. one that leads to an increase in orderliness
A. The one that leads to the release of free energy
Is the following statement true or false based on chemical and biological reactions?
Energetically favorable reactions are those that create disorder by decreasing the free energy of the system to which they belong.
Choose one:
A. false, for all reactions biological and chemical
B. true, for only chemical reactions but not biological
C. true, for all reactions biological and chemical
D. false, for only chemical reactions but not biological
C. true, for all reactions biological and chemical
Determine whether the following statement is true or false: When an enzyme lowers the activation energy for the forward reaction X → Y, it also lowers the activation energy for the reverse reaction Y → X by the same amount.
This statement is
true
Compared to adding heat to the system, what is the advantage of using an enzyme to overcome an energy barrier?
Choose one:
A. An enzyme generates multiple different products using multiple pathways.
B. An enzyme is specific for one desired pathway and end product.
C. An enzyme speeds up a reaction more than heat does.
D. An enzyme can catalyze a reaction in many different ways.
B. An enzyme is specific for one desired pathway and end product
Which is not true of a chemical reaction at equilibrium?
Choose one:
The net concentrations of substrate and product do not change.
Both the forward and reverse reactions have stopped.
The rates of the forward and reverse reactions are equal.
ΔG is equal to zero.
Both the forward and reverse reactions have stopped
Consider the reaction A + B → AB. How is the equilibrium constant expressed for this reaction with two substrates and a single product?
Choose one:
K = [A][B] / [AB]
K = [AB] / ([A] + [B])
K = [AB] / [A][B]
K = ([A] + [B]) / [AB]
the third one K = [AB] / [A][B]
Which statement is true about the removal of a terminal phosphate from ATP?
Choose one:
A. The reaction is associated with a positive change in ΔG°.
B. The reaction is energetically favorable.
C. The reaction is a condensation reaction.
B. The reaction is energetically favorable
The hydrolysis of the terminal phosphate group of ATP is energetically favorable and is coupled to many otherwise energetically unfavorable biosynthetic reactions. Because of its large negative ΔG°, the hydrolysis of ATP is integral to the chemical economy of the cell.
Which statement is true?
Choose one:
A. The heat released by an animal cell comes from the chemical bond energy present in the food molecules it metabolizes.
B. The breakdown of food molecules generates heat, which cells then use to drive the synthesis of large molecules.
C. A cell takes in heat from the environment to power its biosynthetic reactions, thereby obeying the second law of thermodynamics.
D. Cells obey the first law of thermodynamics but are exempt from the second law.
E. A cell generates order by decreasing the entropy of its surroundings.
A. The heat released by an animal cell comes from the chemical bond energy present in the food molecules it metabolizes.
Is the following statement true, false, or impossible to determine?
Because living cells generate order by surviving, growing, and forming complex communities, they defy the second law of thermodynamics.
Choose one:
A. true
B. false
C. impossible to determine
false
In cells ATP is made in the following way: ADP + P —-> ATP
What happens in cells that keeps this reaction from reaching chemical equilibrium?
ATP is consumed
Interpret both Michaelis-Menten and Lineweaver-Burke enzyme kinetics graphs. Use the graphs to identify the value of Km and Vmax. Define Km and Vmax.
look this up
