Unit 10 Flashcards
Distinguish between catabolic and anabolic pathways
- Catabolism is the degradative phase of metabolism in which organic nutrients (fats, carbohydrates, and proteins) are converted into smaller, simpler end products. A catabolic pathway releases energy. Some are conserved in the formation of ATP and reduced electron carriers (NADH and FADH2)
- Anabolism/biosynthesis is when small, simple precursors are built up into larger and more complex molecules, including lipids, polysaccharides, proteins and nucleic acids. They require an input of energy.
Draw the diagram for the catabolic and anabolic pathway
Distinguish between delta G, delta° G, and delta’° G
Delta G: change in free energy for a reaction
Delta G°: standard change in free energy for a reaction - 298K, 1 atm, 1 M
Delta G’°: standard change in free energy for a biological reaction. It is at a pH of 7
What is the sign of Delta G’° if a reaction proceeds in its written direction?
Negative
What is the equation for delta G’°
When Keq is >1, Delta G is ___ and the reaction proceeds ______
Negative and proceeds forward
When Keq is <1, Delta G is ___ and the reaction proceeds ______
Positive and proceeds backwards
When Keq is 1, Delta G is ___ and the reaction proceeds ______
Zero and is at equilibrium
Do Problem 2 (be sure to look a the units to make sure they align)
What are the units for delta G’°?
J/mol or kj/mol
How to convert between kj and J
kj–> J (multiple by 1000)
J –> kJ (divide by 1000)
Do Problem 3 (be sure to make your units match up)
How to undo ln?
ln(keq) = x
e raised to the power of x will give you keq
Do Problem 6 (be sure to make your units match up)
What are the units for Keq?
It is unitless
Compare the free energy content of acid anhydride and ester bonds
Acid anhydride bonds have a lower delta G meaning they have more free energy
Write the Gibbs equation that relates the delta G and delta G’°
delta G = delta G’° + RTln(Q)
Q is products/reactants
*the products and reactants are multiplied by each other
Which term in the Gibbs equation can be used to predict whether a reaction will proceed? Why do we use this term?
It is delta G NOT delta G’°. When delta G is negative, the reaction will occur spontaneously
The reason we talk in terms of delta G’° as a matter of convenience because we can just look up this values. However, delta G is variable depending on Q.
What does delta G tell you about the rate of the reaction?
Nothing
What effects do enzymes have on delta G?
No effect
Draw the structure of ATP, you may use A to abbreviate the structure of the nitrogenous base
Give at least two reasons why delta G’° is such a large negative number for the reaction
1) Charge separation resulting from hydrolysis relieves electrostatic repulsion between the negative oxygens (making the product, ADP, more stable and lower in energy)
2) Inorganic phosphate is resonance stabilized (product is more stabilized meaning it has a lower energy. It is more resonance stabilized as an inorganic phosphate than in the ATP molecule)
Although the free-energy change for ATP hydrolysis is -30.5 kJ/mol, ATP is kinetically stable in water in the absence of enzymes. Suggests why.
Although spontaneous, ATP still has a high activation energy and does not have enough energy to proceed with the forward rxn without an input of energy Energy is still required in general to break a bond
Why are thioester, but not oxygen ester, high energy bonds?
In terms of hydrolysis. Draw the thioester and the oxygen ester
- Before the thioester undergoes hydrolysis, it has no resonance so it has a more positive delta G, however, once it goes to hydrolysis, there is resonance so its product is extremely low. This makes it release a lot of energy
- For an oxygen ester, there is resonance before and after so both the product and the reactant were relatively stable, therefore this reaction won’t free up as much energy
Is it possible for a reaction with a positive delta G’° to be driven by a coupled reaction which has a negative delta G’°. Explain why this can occur.
This can occur because delta G’° values are additive with one another, so the reaction that has a positive delta G’° can move forward
Do Problem 9:
Do Problem 12:
Do Problem 13:
Distinguish between a reducing agent (reductant) and an oxidizing agent (oxidant)
- Reducing agent: The reducing agent is losing electrons. By losing electrons, it is being oxidized. By being oxidized, that means it is reducing the other species
- Oxidizing agent: The oxidizing agent is gaining electrons. By gaining electrons, it is being reduced. By being reduced, it must be oxidizing the other species.
Define standard reduction potential E°and E’°
- E° is the tendency of a reductant, to lose electrons at standard conditions
- E’° is the same definition but at biologically standard conditions
Which half reaction contains the strongest oxidant - one with a more positive E’°, or one for which it is more negative
Large positive E
Electrons tend to flow to the electrons with the more positive E
Which half reaction contains the strongest reductant - one with a more positive E or one with a more negative E?
Large negative E
Electrons will not flow in this direction
Go to slide 30. Pick two half reactions from the table and identify which half reaction contains the strongest oxidant and which contains the strongest reductant then specifically identify the strongest oxidant and reductant in each of these half reactions
What is Faraday’s Constant
96.5 (kJ/V x mol)
What are the units for delta E’°
Volts
Really practice questions 28, 30, 32, 33
Be careful, when determining which one is your strong oxidant and which one is your strong reductant, determine it before you flip anything. So the one that is more negative is your reducing agent and the one that is more positive is your oxidizing agent
Are FAD and NAD+ reducing agents or oxidizing agents?
Oxidizing agents because they are oxidizing the other group and accepting electrons
Draw NAD+ and how it accepts electrons to become NADH. How many electrons and protons does it accept?
Accepts 2e- and 2H+
Draw FAD and how it become electrons to become FADH2. How many electrons and protons does it accept?
Accepts 2e- and 2H+
What words do the letters of NAD+ stand for?
Nicotinamide Adenine Dinucleotide
Using words, not structures, show how the component parts of the molecule are arranged and linked together for NAD+?
Adenine – Ribose – Phosphate – Phosphate – Ribose — Nicotinamide
How is the structure of NADP+ different from NAD+? Draw it
On the 2nd carbon of the ribose (near the adenine) there is a phosphate group on that OH
Distinguish between the physiological role of NADH and NADPH
- NADH generally function in metabolism such as cellular respiration
- NADPH generally functions in anabolism/biosynthesis
They are both reductants
How can redox reactions involving NAD+/NADH be monitored in vitro?
- When reduced, NAD+ is NADH. NADH absorbs at a wavelength of 340 nm. Therefore, if you check to see if there is absorbance at 340 nm, then you must have NADH present
What words do the letters FMN stand for?
Flavin mononucleotide
Using words, not structures, show how the components of FAD are arranged and linked together
Adenine – Ribose — Phosphate — Phosphate – CH2, HCOH, HCOH, HCOH, CH2 — isoalloxazine ring
What is coenzyme A?
A coenzyme used in the transfer of acyl groups in metabolic reactions
(as opposed to electrons)
What makes of FMN?
CH2 HCOH HCOH HCOH CH2 — isoalloxazine ring
Define monosaccharide in terms of functional groups and empirical formula
- A simple sugar that consists of a polyhydroxy aldehyde or ketone
- Empirical Formula: (CH2O)n
Distinguish between aldose and ketose sugars
- If the carbonyl group is at the end of a carbon chain, the monosaccharide is an aldose
- If the carbonyl group is in the middle or at any other position, the monosaccharide is a ketose
Using a structural formula of the tupe ROH, represent the reaction of an alcohol with an aldehyde to form a hemiacetal and with a ketone to form a hemiacetal
- Just remember that the OH will come in, attack the carbon, and push electrons onto that oxygen. The oxygen will also end up getting that Hydrogen
- The same thing would occur for the ketal
- You lose the H both times when you do the reaction
Show that a pyranose ring results from intramolecular hemiacetal formation in glucose. Show that a furanose ring results from the intramolecular hemiketal formation in fructose.
- D-Glucose has 6 carbons and is an aldose. Just remember that the third carbon is alternate. And that the fifth carbon is the one that will attack the aldehyde group
- Fructose has 6 carbons as well, except it is a ketose, so its second carbon is the carbon that will be attacked. You have two CH2OH groups on both sides of the fructose molecule. VERY IMPORTANT: when drawing your structure, put the third carbon in the correct place! It will be on the right side for fructose
- The OH is typically on the right side except for the third carbon for the d-glucose and the third carbon for the fructose as well
Note: THe ring forms of monosaccharides are always in equilibrium with the open chain form i.e. with the free aldehyde or ketone
What is the name of the ring formed with glucose?
Pyranose
What is the name of the ring formed with fructose?
Furanose
Indicate the nature of the most prevalent glycosidic linkage
Alpha, 1-4
Indicate the nature of the glycosidic linkage at the branch points
alpha, 1-6
What is meant by the reducing end? Point out the reducing and non-reducing ends on glycogen
It is the end where you have a free carbon that isn’t involved in the “o-glycosidic bond”. It’s free to act as a reductant to keep building glycogen
What are the two phases of glycolysis?
- Investment phase/Prepatory (first 5 steps)
- Payoff phase (last 5 steps)
What is invested in the prepatory phase?
- Two molecules of ATP
Name two molecules in which energy is conserved in the payoff phase
- Much of this energy is conserved by the coupled phosphorylation of 4 molecules of ADP to ATP (ATP is conserved)
*technically the NET yield is only 2 ATPs then - Energy is also conserved in the payoff phase in the formation of two molecules of NADH per molecule of glucose
The glycolysis pathway is more complex than would be needed chemically because the cell membrane must be impermeant to all the intermediates. How is this accomplished?
- All intermediates are phosphorylated
- Glycolysis occurs in the cytoplasm. These intermediates being phosphorylated prevents them from leaving the cell membrane and escaping glycolysis
Draw out the process of glycolysis, writing all names, showing all intermediates. and explaining the type of reactions that catalyze the formation of those intermediates
Mark on your diagram the two reactions in which ATP is used in Phase 1. What types of enzymes catalyze this reaction?
Steps one and three
Kinases
Mark on your diagram the two reactions in which ATP is generated in Phase 2. Name the two compounds which donate phosphate to ADP
- 1,3- Bisphosphoglycerate (to 3-phosphoglycerate)
- Phosphoenolpyruvate (to generate pyruvate)
To what kind of energy rich group is the aldehyde of glyceraldehyde 3-phosphate converted in the oxidation step of glycolysis? Circle this group on the structure
Mixed anhydride
Name the type of linkage by which the other phosphate group is linked in this molecule
Phosphoester
Estimate the delta G’° of hydrolysis of these two phosphate groups by finding similar groups
-49.3 and -9.2
Find the delta G’° of the second energy rich molecule which formed ATP in glycolysis. How does it compare with the delta G’° of other compounds in the table?
- The molecule itself is phosphoenolpyruvate and its delta G is -61.9. It has a very high energy yield compound to other compounds. This energy release is able to form ATP, which is more stable than the phosphoenolpyruvate. Since ATP is a lot more stable, it is essentially irreversible to go back into phosphoenolpyruvate because it would require a lot of energy to get to that point again
Indicate the general type of reaction catalyzed by kinases:
- Add or remove phosphates from a molecule
Indicate the general type of reaction catalyzed by isomerases:
- Isomerases catalyze reactions that convert one isomer into another.
Dehydrogenases
- Dehydrogenases catalyze reactions that involve the transfer of hydrogen atoms, along with their associated electrons, from substrates (reducing agent) to coenzymes such as NAD+ or FAD (oxidizing agent).
Mutases
- Mutases catalyze reactions that facilitate the intramolecular rearrangement of functional groups within a molecule
Aldolase
Form an aldol functional group in a molecule
Enolase
Enolase catalyzes reactions that involve the conversion between keto and enol forms of certain compounds, typically involving the elimination of water.
One of the four kinase catalyzed reactions in glycolysis is reversible under cellular conditions. Which one?
Step 7
1,3-Bisphosphoglycerate –> 3-Phosphoglycerate + ATP
Show how glyceraldehyde 3-phosphate dehydrogenase uses a strategy involving a covalent enzyme-bound intermediate as a mechanism of energy coupling (i.e. the energy released during oxidation is used to make a high energy mixed anhydride bond). Note that the product of the oxidation is a thioester which is subsequently cleaved by Pi
Draw it
How does it end up energetically favorable to have the Glyceraldehyde 3 Phosphate Dehydrogenase reaction?
- Reducing NAD+ and oxidizing G3P is favorable
- Adding the phosphate group at the end is not favorable
- In sum, it ends up being slightly unfavorable (Positive delta G) but since we are constantly using 1.3-bisphosphoglycerate, the reaction is driven forward anyways
*this is a great way to add a phosphate without using ATP
What kind of functional group is the product of oxidation that needs to be cleaved by the phosphate?
A thioester gets cleaved by the Pi group
In order for glycolysis to continue, NAD+ must be regenerated. How?
- If it’s aerobic, it will go through the ETC and regenerate NAD+
- If its anaerobic, it will go through either ethanol *yeast or lactic acid fermentation to create lactate *humans
How is NAD+ regenerated under aerobic conditions?
ETC
Draw the reactions by which NADH is oxidized to NAD+ in
1) anaerobic muscle
2) anaerobic yeast
- Muscle means to draw the pathway to make lactate
- Yeast means to draw the pathway to make ethanol
In every metabolic pathway in the cell there is at least one reaction that is far from equilibrium because of the relative low activity of the enzyme that catalyzes the reaction. The reaction is therefore said to be enzyme-limited, and because its rate limits the rate of the whole reaction sequence, the step is called hte rate-limiting step in the pathway. These rate-limiting steps are highly exergonic and irreversible. Enzymes that catalyze these exergonic, rate-limiting steps are commonly the target of metabolic regulation.
The enzyme is PFK-1 in glycolysis
PFK-1 Is the key regulatory enzyme in glycolysis. How is it regulated?
Allosterically
Name 5 substances that regulate the activity of this enzyme and explain why their action is logical. Note the regulatory logic of fructose 2,6- Bisphosphate will be discovered extensively in future units
- Upregulation:
ADP
AMP
Fructose 2,6-Bisphosphate - Downregulation:
Citrate
ATP
What is the overall net reaction for glycolysis:
Glucose + 2 ATP + 2 NAD+ + 4 ADP + 2 Pi –> 2 Pyruvate + 2 ADP + 2 NADH + 2H+ + 4 ATP + 2H2O
