L09: Enzymes, Biochemical Pathways, and Energetics of Chemical Reactions

Question 1

What is an enzyme?

Answer 1

Biota use enzymes to facilitate chemical reactions (rxn).

To react, e- within established bonds must be excited so they change this bonding patterns.
Need a nudge to get going.

Question 2

In which biomolecule class are most enzymes classified?

Answer 2

proteins

Question 3

What is Ea?

Answer 3

Reactions need a nudge to get going. The magnitude of this nudge is termed a reaction’s activation energy (Ea).

Question 4

What do enzymes do to the Ea of a chemical reaction?

Answer 4

Enzymes catalyze chemical reactions by ↓ Ea making a rxn go.

lower Ea to increase reaction

Question 5

How does the Ea compare in a chemical reaction with and without an enzyme?

Answer 5

Ea is greater in chemical reactions without enzyme

Question 6

In which three ways can enzymes lower Ea?

Answer 6

Enzymes lower Ea by:
1) align substrate functional groups so they can react (dehydration rxn)
2) stretch substrate straining bonds (hydrolysis rxn)
3) create microenvironments (↓ pH)

Question 7

Which name is given to reactants of enzyme-catalyzed reactions?

Answer 7

substrates to products

Question 8

Which region of an enzyme do these reactants bind? Once they do, what happens to the enzyme as a result?

Answer 8

bind with weak bonds in the protein active site. Once in place, enzyme protein “bear hugs” substrate and begins catalysis cycle/stages.

Question 9

What does enzyme affinity for substrate means?

Answer 9

Enzymes have affinities for specific substrates because the
shape of the substrate fits into the enzyme’s active site.

They search for substrate that fits perfectly.

Question 10

Based on enzyme affinity, how many chemical reactions would you expect a typical enzyme to catalyze?

Answer 10

one enzyme tends to only interact with one (or a few) substrate.

Question 11

An individual enzyme molecule is not destroyed during catalysis. What does this mean for the ability of the enzyme to catalyze the same reaction again?

Answer 11

A single enzyme molecule can catalyze numerous cycles of the same rxn because it is not destroyed during the catalysis cycle.

Question 12

What are the stages of the catalysis cycle?

Answer 12

1. substrates enter active site
2. substrates are held in active site by weak interactions
3. active site can lower Ea and speed up reaction
4. substrates are converted to products
5. products are released
6. active site is available for two new substrate molecules

repeat

Question 13

Which factors impact the rate of enzyme activity?

Answer 13

Rate of enzyme activity depends on the ratio of [substrate] to open [enzyme active sites].

Question 14

Which three of these factors are particularly important in optimizing enzyme activity?

Answer 14

temperature, pH, and salinity

Question 15

What happens to enzyme activity if suboptimal conditions exist?

Answer 15

Enzyme activity is optimized to work better within environs with optimal temperature, pH, salinity

Question 16

If conditions depart markedly from optimal levels enzyme function will cease entirely. Propose an answer explaining why based on what you know about protein structure and folding.

Answer 16

An enzyme is a protein that is optimized best to work in specific body temperature. too hot or too cold can denature protein and your body won’t be able to carry out enough enzyme activity to sustain life

Question 17

Which chemical reaction does Pepsin carry out and which conditions are optimal for it to have the greatest activity?

Answer 17

Our Pepsin hydrolyzes proteins in the stomach best at 37°C and pH=2

Question 18

What does enzyme inhibition mean?

Answer 18

A substance that blocks the action of an enzyme.

Question 19

1. How do competitive and noncompetitive enzyme inhibitors differ in their mechanism of inhibition. Do you see how someone might be harmed by ingesting substances that act as enzyme inhibitors?
2. In a similar way, do you see how inhibitors might be used therapeutically by decreasing overactive enzyme activity?

Answer 19

1. Enzymes are inhibited by competitive (blocks active site) and non-competitive (deforms active site by attaching
   elsewhere) inhibitors either irreversibly or reversibly
2. serves as a control

Question 20

What is allosteric activation?

Answer 20

Allosteric activators stabilize active form of allosteric (4°
proteins) enzymes.

Question 21

What is allosteric inhibition?

Answer 21

Allosteric inhibitors stabilize inactive form of allosteric
(4° proteins) enzymes.

Question 22

What is feedback inhibition?

Answer 22

Feedback inhibition occurs when products of a pathway inhibit enzymes that catalyze reactions in early portion of the pathway.
Often occurs by reversible non-completive inhibition.

Question 23

Would you be able to discern among these methods of enzyme regulation based on written descriptions and/or images similar to those in the book?

Question 24

What is a biochemical pathway?

Answer 24

A biochemical pathway is a group of chemical reactions
linked together in a series.

The product(s) of a preceding reaction become reactant(s)
of the subsequent reaction (e.g., mevalonic acid becomes
melanovate-5-phosphate).

Question 25

What role do enzymes in biochemical pathways?

Answer 25

Enzymes catlyze reactions in biochemical pathways

Question 26

What is the rate-limiting reaction of a pathway?

Answer 26

Biochemical reactions proceed at a given rate; some reactions are faster than others.

The slowest reaction in a pathway is the rate-limiting reaction of that pathway (e.g., HMG-CoA ➟ Mevalonic acid).

Question 27

Why are pharmacologists interested in rate-limiting reactions in pathways?

Answer 27

The rate-limiting reaction is often targeted by pharmaceuticals to modify a pathway (e.g., statins competitively inhibit HMG-CoA
Reductase ↓ cholesterol synthesis)

Question 28

Why are statin drugs prescribed to patients?

Answer 28

to lower their total cholesterol and reduce their risk of a heart attack or stroke.

Question 29

Generally speaking, how do statin drugs decrease cholesterol synthesis in humans?

Answer 29

slowing down the liver’s production of cholesterol

Question 30

Define energy.

Answer 30

Energy is the capacity to do work.

Question 31

How does energy impact matter?

Answer 31

It can change the position, composition, and temperature of matter.

Question 32

What are the two states of energy and how do they differ from each other?

Answer 32

Energy has two states:

Potential energy is stored energy that has capacity to do work (e.g., membrane potential).

Kinetic energy is actively doing work.

Question 33

What are the five forms of energy?

Answer 33

Energy exists in different forms: solar, electrical, mechanical, chemical, and heat.

Question 34

What is chemical energy?

Answer 34

Chemical energy is found within chemical bonds.
It can transfer to other matter when bonds break.

Question 35

Which form of energy has the greatest capacity to do biological work?

Answer 35

Forms of energy differ in their ability to perform work.
Solar energy has a greater potential to perform work than heat

Question 36

Does heat typically perform biological work?

Answer 36

not usually

Question 37

What is thermodynamics?

Answer 37

study of energy transfer and transformation

Question 38

What does the First Law of Thermodynamics state?

Answer 38

First Law: Energy can be transferred and transformed but
it cannot be created nor destroyed.

Question 39

How does the first law pertain to the processes of photosynthesis and cellular respiration?

Answer 39

Chloroplasts transform solar energy into chemical
energy (e.g., sugars) during photosynthesis.

Mitochondria transform chemical energy in sugar to ATP.
ATP powers biological work (e.g., active transport).

Question 40

Which form of energy is always given off during an energy transformation because of its lack of efficiency?

Answer 40

No transformation is 100% efficient, so heat is produced.

Question 41

What does the Second Law of Thermodynamics state?

Answer 41

Energy transfer during transformation increases the entropy (measure of disorder) within the universe.

Energy harnessed to do work is required to maintain order

Question 42

As our solar system ages more and more of our solar energy is transformed to heat. What does this do to the quantity of energy available to power biological work and order? How does this fact change the amount of entropy in the system?

Answer 42

Heat, limited in its ability to perform biological work,
does little to maintain biological order.

Consequently, as more ‘higher order’ forms of energy (e.g.,
solar) are transformed to heat, less energy in the system is
available to maintain biological order (entropy ↑).

Question 43

Eventually the sun will cease to emit energy. Assuming life on Earth was not destroyed as the sun goes supernova prior to dying out (this is a false assumption), why will life on Earth parish? Consider the first and second laws in your answer.

Question 44

What does ΔG mean?

Answer 44

Free energy (G) is the energy that is available to do work.
ΔG is the “change in free energy.” ΔG = GFinal – GInitial

Question 45

How do exergonic and endergonic reactions compare in regards to: the sign of their ΔG value, whether or not energy is given off or required to drive the reaction, whether or not the reaction is spontaneous, and whether or not the reactants or products are more or less stable based on their free energy level?

Answer 45

Reactions that release energy are exergonic (–ΔG)(3 – 10 = –7).
Such reactions are spontaneous (occur without outside energy) because the reactants are less stable and have more free energy than the products

Reactions that require energy are endergonic (+ΔG)(8 – 2 = 6)
Such reactions are not spontaneous because the products are less stable and have more free energy than the reactants

Question 46

1. Overall, is photosynthesis exergonic or endergonic?
2. Overall, is cellular respiration exergonic or endergonic?

Answer 46

1. endergonic
2. exergonic - some of the free energy from glucose is used to ‘recharge’ ATP and some is ‘lost’ as heat.

Question 47

What is reaction equilibrium?

Answer 47

the state in which both the reactants and products are present in concentrations which have no further tendency to change with time, so that there is no observable change in the properties of the system.

Question 48

1. What does ΔG equal when a reaction has reached equilibrium?
2. Is this state desirable in metabolic pathways of biota? Why or why not?

Answer 48

Reaction equilibria are not desirable in biota because at equilibrium ΔG=0; i.e., no more free energy to do work

Question 49

What does the steady state refer to? Why must biota maintain the steady state?

Answer 49

Biota must have metabolic pathways that maintain –ΔG (left) otherwise they can’t do work and die (right).

Seeking to maintain –ΔG is called the metabolic steady state

Question 50

What is the sign of ΔG during the steady state?

Answer 50

exergonic –ΔG

Question 51

Which three activities do biota carry out that permit them to maintain the steady state and a –ΔG?

Answer 51

To maintain a steady state requires:

1) ingesting reactants (aka food)
2) using products of one rxn as reactants in subsequent rxns
within biochemical pathways
3) excreting waste products

Question 52

Why must biota carry out exergonic reactions?

Answer 52

to move energy out of “storage” in one molecule, such as a sugar or fat, and into an active form such as ATP

Question 53

Hydrolysis of which molecule is a routine exergonic reaction biota use to power endergonic reactions?

Answer 53

ATP hydrolysis

Question 54

In what two ways can the hydrolysis of ATP drive an endergonic reaction?

Answer 54

1. may facilitate a reaction by exciting e- to form new bonds
2. facilitate a rxn via phosphorylation (adding – ℗) of reactants, changing their shape

Question 55

What does phosphorylation mean?

Answer 55

A biochemical process that involves the addition of phosphate to an organic compound.

Examples include the addition of phosphate to glucose to produce glucose monophosphate and the addition of phosphate to adenosine diphosphate (ADP) to form adenosine triphosphate (ATP).

Question 56

Eventually cells will run out of ATP. Which process do most cells use to recharge ADP ➟ ATP?

Answer 56

cellular respiration