BIOCHEM 2EE3 Lecture Notes - Lecture 6: Tetrahedral Carbonyl Addition Compound, Serine Protease, Catalytic Triad

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17 Sep 2016

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A catalyst is a substance that increases the rate, or velocity, of a chemical reaction without itself being consumed in the reaction process. A thermodynamically favourable process is not made more favourable, nor is an unfavourable process made favourable, by the presence of a catalyst: the equilibrium state is just approached more quickly in the presence of a catalyst. Catalysts accelerate the approach to equilibrium for a given reaction- catalysts do not change the thermodynamic favourability of a reaction. Transferases catalyze transfer of functional groups from one molecule to another. Lyases catalyze removal of a group from, or addition of a group to, a double bond, or other cleavages involving electron rearrangement. Ligases catalyze reactions in which two molecules are joined. How enzymes act as catalysts: principles and examples. Role of a catalyst is to decrease deltag by facilitating the formation of the transition state. Interaction has extraordinary specificity through complementary binding interactions (lock and key model example)

Related Questions

Problem A: This is a very simpllistic approach to protein folding, which ignores solvent and volume effects, but it allows us to practice what we have learned about thermodynamics and kinetics. Enzymes are long chains of amino acids that have to fold in the proper way so as to exhibit enzyme activity. They can catalyze certain reactions. Let us pick a reaction in the human body at 37 C, we will call it enzyme X.

1) What is the expected sign of delta G for the reaction that forms enzyme X starting from the long chain of amino acids at 37 C?

2)What is the value of K(eq) for the reaction at 37C, assuming the system is reversible?

3)Based purely on the drawing (unfolded and folded (native form)) what is the expected sign of delta S for the reaction that forms enzyme X at 37 C?

4)What is the expected sign of delta H for the reaction that forms enzyme X at 37 C?

5) Under what conditions is the folded form NOT thermodynamically favored? always favored, high temperatures, never favored, low temperatures

6)Let's say that enzyme X is the catalyst responsible for breaking starch down to individual glucose molecules. What of the following things can happen to the starch and enzyme system if you rainse the temperature?

a-the rate of the reaction of starch going to glucose will increase

b-nothing should happen since a catalyst does not affect the equilibrium

c-the enzyme could stop working effectively becauset the folded form would stop being made and would start to unravel if the process is reversible

d-the equilibrium constant will get bigger to favor the glucose side more.

1. C6H12O6 + 6O2 Ã 6CO2 + 6H2O Glucose is being _____ to _____ and oxygen is being _____ to _____. a. oxidized; carbon dioxide; reduced; water b. oxidized; water; reduced; carbon dioxide Incorrect c. reduced; water; oxidized; carbon dioxide d. reduced; carbon dioxide; oxidized; water

2. Which of the following stages in the breakdown of the piece of toast you had for breakfast generates the most ATP? a. the citric acid cycle Incorrect b. glycolysis c. the digestion of starch to glucose d. oxidative phosphorylation

3. Which of the following is a catabolic pathway? a. gluconeogenesis b. production of starch Incorrect c. glycolysis d. production of glycogen

4. Per molecule, the oxidation of a fatty acid results in _____ energy storage than the oxidation of glucose. a. the same b. less Incorrect c. more d. None of the above; fatty acids cannot be oxidized.

5. Of the eight reactions in the citric acid cycle, how many are oxidation-reduction reactions? a. one b. two c. three d. four e. five

6. The process of glycolysis transfers the energy in sugar molecules into the stored energy of activated carriers such as ATP and NADH. Which statement is true about glycolysis? a. Only eukaryotic organisms do glycolysis. b. The ten reactions of glycolysis are identical in all eukaryotic cells, but are different in prokaryotic cells due to their diverse metabolic strategies. Incorrect c. The ten reactions of glycolysis are identical in almost all living organisms on the planet. d. There are many ways to oxidize glucose and transfer energy into activated carriers; the diversity of organisms on the planet is reflected in the diversity of their mechanisms of glycolysis.

7. Referring to the sentence completed in #13 above, the purpose of the latter reaction (in active muscle cells) is to _____. a. accumulate lactic acid in the cell, which provides additional energy for the production of ATP Incorrect b. slow down glycolysis until oxygen becomes available again c. accelerate the Krebs cycle, which will restore the oxygen supply d. regenerate NAD+ so that glycolysis can continue in the absence of oxygen

8. What are the products of the citric acid cycle? a. carbon dioxide, NADH, FADH2 and GTP b. carbon dioxide, NAD+, FAD and GTP c. NADH, FADH2, and acetyl CoA Incorrect d. carbon dioxide and water

9. Which statement is true about enzymes? a. Enzymes catalyze chemical reactions because they make inherently endergonic reactions exergonic. b. Each enzyme in a cell can catalyze many different chemical reactions involving chemically different substrates. Incorrect c. Enzymes can only catalyze reactions in one direction. d. After catalyzing a reaction, an enzyme is permanently altered and can no longer bind substrate. e. None of the above is true. 1

10. âG measures the change in free energy in a system as it converts reactant (Y) into product (X). When [X] = [Y], âG is equal to _____. a. RT b. ÎGÂ° + RT c. ÎGÂ° d. ln [X]/[Y]

11. The âGÂ° for the hydrolysis of ATP is -7.3 kcal/mol. What conditions in the cell would lead to a âG for ATP hydrolysis of -11 kcal/mol? a. An increase in the ATP/ADP ratio b. An increase in anabolic activity in the cell c. Transport of ATP out of the compartment where the reaction is occurring Incorrect d. A decrease in the ATP/ADP ratio

12. In the first reaction of glycolysis, a phosphate transferred from ATP to a glucose molecule to produce glucose-6-phosphate and ADP. Under conditions existing in the cell, the free energy change for this reaction is -8.0 kcal/mole. Which of the following statements is true? Recall that the âGÂ° for the hydrolysis of ATP is -7.3 kcal/mol. a. Glucose concentrations in the cell are always low, making this reaction more favorable than would be expected. b. This reaction is less favorable than would be expected, given the âGÂ° of ATP hydrolysis. c. Glucose-6-P concentrations in the cell are very low relative to glucose concentrations, making the reaction more favorable than would be expected. d. The âGÂ° for the addition of a phosphate to glucose must be -0.7 kcal/mole.

13. Protein E can bind to two different proteins, S and I. The binding reactions are described by the following equations and values: E + S --> ES Keq for ES = 10 E + I> EI Keq for EI = 2 Given the equilibrium constant values, which one of the following statements is true? a. When S is present in excess, no I molecules will bind to E. b. E binds I more tightly than S. c. The binding energy of the ES interaction is greater than that of the EI interaction. d. Changing an amino acid on the binding surface of I from a basic amino acid to an acidic one will probably make the free energy of association with E more negative.

1.When something appears blue, it is absorbing all colors except__________.

yellow

blue

red

green

orange

2.During heavy exercise, lactic acid can build up in ourmuscles. Why? How does this resemble the metabolism of bacteria andyeast?

lactic acid is results from insufficient oxygen during sugarmetabolism; it is fermentation

lactic acid accumulates when we are dehydrated; bacteria andyeast use the same pathway

lactic acid is built up from carbon dioxide; bacteria and yeaststore energy in this way

3.Why must a cell keep a similar concentration of dissolvedsubstances with the fluid surrounding them?

to avoid dilution of potential energy

to avoid osmotic imbalance and rapid gain or loss of water

to maintain the correct amount of dehydration and hydrolysis

4.What is entropy?

the amount of energy in a system

the amount of disorganization

the amount of organization

5.Burning a log is the reverse reaction found in photosynthesis.What products would be formed in burning a log?

carbon dioxide and water

glucose and oxygen

oxygen and carbon dioxide

oxygen and water

6.The main reason that cellular respiration needs to occur stepby step instead of a single, big reaction is

cells don't store enough oxygen

too much energy would be released for the cell to harness

cells don't have many mitochondria.

cells produce the enzymes needed for cellular respiration veryslowly

7.Enzymes are catalysts because they operate to:

raise activation energy

lower activation energy

supply activation energy

supply the reactants

8.When ATP powers a reaction it becomes ADP. The ADP

can reform ATP by an exergonic reaction

is a waste product for lysosomal breakdown

can reform ATP by an endergonic reaction

can reform ATP by an oxidation reaction

can reform ATP by an equilibrium reaction

9.The energy source that drives photosynthesis is

water

glucose

carbon dioxide

oxygen

sunlight

10. What is the process by which enzymes regulate their ownactivity?

osmosis

self-propulsion

feedback inhibition

11.Coupled reactions are reactions in which a

endergonic reaction drives a spontaneous reaction

exergonic reaction drives a spontaneous reaction

endergonic reaction drives an exergonic reaction

exergonic reaction drives an endergonic reaction

12.How is water used in photosynthesis?

as a substrate for ATP synthase

as an electron donor

to combine with ADP forming ATP

as an electron acceptor

13.Why are the âDark Reactionsâ of photosynthesis referred to asâDarkâ?

they do not require light

they can only occur at night

they generate excess sugar and the leaves turn brown

14.What is the difference between potential and kineticenergy?

potential is stored, kinetic is being used

potential is being used, kinetic is ready to be used

potential is negative, kinetic is positive

15.The products of cellular respiration are

carbon dioxide, water, and ATP

glucose, water, and ATP

glucose, carbon dioxide, and ATP

oxygen, ATP, and water

carbon dioxide, glucose, and water

16.All of the following are correct about energy except:

The biological world gets its energy from the sun.

Chemical bonds store potential energy.

A boulder perched on a hill has kinetic energy.

Energy is defined as the ability to do work.

All forms of energy can be converted to heat.

17.What is needed for the end product of glycolysis, pyruvate,to enter the citric acid cycle?

More glucose for energy

ATP

Oxygen

Carbon dioxide

18.The enzyme that forms a transmembrane channel in mitochondriaand phosphorylates ADP

a carrier protein

ATP synthase

acetyl CoA

19.Fermentation is most common in

plants

microorganisms

animals

20.During adsorption of sunlight by photosystems, H+ ions aregenerated. Where do they come from? What are they used for?

from the breakdown of sugar; they help form water

water; they help form sugar

from carbon dioxide; they help dissolve NaCl

21.Glycolysis

does not use oxygen

uses oxygen

uses carbon dioxide

22.Photosynthesis is

not dependent on chlorophyll

a process that produces glucose and oxygen

a process that produces water and carbon dioxide

23.Breakdown of glucose generates many ATP molecules, each ofwhich can be used independently. Why is ATP ideally suited to powerbiological reactions?

ATP has many hydrogen bonds

ATP has enough energy to power one biological reaction

ATP readily dissolves in water

24.Objects that are not actively moving but have the capacity todo so are said to possess:

kinetic energy

entropy

potential energy

living energy

25.The first stage of cellular respiration, called ___________,takes place in the cytoplasm of the cell and needs no oxygen.

photorespiration

citric acid cycle

glycolysis

oxidation

26.Diffusion

requires energy

utilizes proteins to move molecules across a membrane

moves molecules against a concentration gradient

does not require energy

cannot occur without a membrane present

27.What is the name of the molecule on which an enzymeworks?

substrate

monomer

polymer

28.ATP contains

phenylalanine

two phosphate groups

three nitrate groups

three phosphate groups

29.How does chlorophyll function in photosynthesis?

by absorbing carbon dioxide

by absorbing the sun's energy

by absorbing water

30.Objects that are moving are said to possess:

living energy

potential energy

entropy

kinetic energy

31.The respiration pathway that evolved first is probably

glycolysis

aerobic respiration

citric acid cycle

32.The energy source for the process of photosynthesis is

oxygen

sunlight

carbon dioxide

chlorophyll

glucose

33.Burning wood generates heat and light. What type of reactionis this?

exergonic

kinetic energy

endergonic

potential energy

equilibrium

34.What is meant by a âcoupled reactionâ in terms of energy?

many poymers are built simultaneously

energy released by one reactions powers another reaction

some reactions occur in the same organelle

35.The First Law of Thermodynamics states:

energy is constantly being created by entropy events

energy can be changed from one form to another, but cannot becreated or destroyed

energy can be used and then destroyed because of entropy'sactions on it

energy can be destroyed while it is producing entropy

36.How do we dispose of the carbon derived from the glucose thatis metabolized during respiration?

by breathing out

via our urine

it is broken down in lysosomes

37.Both plant and animal cells have mitochondria because theyboth

carry on respiration

carry on photosynthesis.

require water

38.What is Activation Energy?

the energy needed to initiate a reaction

the energy that transports water into cells

potential energy

39.If you put a plant in a chamber and shine a light on it

oxygen will decrease and carbon dioxide will increase

oxygen will increase and carbon dioxide will decrease

oxygen and carbon dioxide will increase

oxygen and carbon dioxide will decrease

40.What are the inputs and the output molecules for the overallphotosynthetic process?

input sugar and oxygen; output carbon dioxide and water

input oxygen and water; output sugar and carbon dioxide

input carbon dioxide and water;output sugar and oxygen

41.What kind of reaction is photosynthesis?

endergonic

kinetic energy

exergonic

potential energy

equilibrium

42.In the process of glycolysis, glucose is cleaved into a pairof three-carbon molecules called

lactate

pyruvate

acetyl CoA

ATP

alcohol

43.Entropy is

order

disorder

complexity

Both order and disorder are correct

Both complexity and disorder are correct

44.Glycolysis takes place in the _____________ and the citricacid cycle and electron transport chain take place in the___________.

cytoplasm; endoplasmic reticulum

mitochondria, chloroplast

mitochondria; cytoplasm

cytoplasm; mitochondria

45.The organelle that carries out photosynthesis in plants isthe

mitochondria

chloroplast

ribosome

chlorophylllysosome

46.The energy to power the Calvin cycle comes from

cellular respiration

oxygen

the light reactions of photosynthesis

47.Which of the following can be broken down into intermediateproducts that enter cellular respiration?

Proteins

Lipids

Carbohydrates

All of these.

48.When cellular product levels get too high, the responsibleenzyme is inhibited. This is an example of

promotion

denaturation

equilibrium

a coenzyme

feedback inhibition

49.How is respiration the opposite of photosynthesis?

respiration breaks sugar down to carbon dioxide; photosynthesisbuilds sugar from carbon dioxide

respiration builds sugar from carbon dioxide; photosynthesisbreaks sugar down to carbon dioxide

respiration requires energy input; photosynthesis gives offexcess energy

50.The molecule that absorbs sunlight for photosynthesis is

oxygen

carbon dioxide

chlorophyll

glucose

sunlight

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BIOCHEM 2EE3 Lecture Notes - Lecture 6: Tetrahedral Carbonyl Addition Compound, Serine Protease, Catalytic Triad

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