Exam 2: Enzymes

Question 1

Activation energy

Answer 1

energy required to weaken and break existing bonds.

Question 2

Active site

Answer 2

the portion of an enzyme that binds to the substrate. The mouth or pocket of that specific shape is accessible to the substrate.

Question 3

Catalyst

Answer 3

a substance that increases the rate of a chemical reaction without itself undergoing any permanent chemical change.

Question 4

Chemical Reaction

Answer 4

he processes by which chemicals interact to form new chemicals with different compositions

Question 5

Cofactor

Answer 5

A cofactor is a non-protein chemical compound or metallic ion that is required for an enzyme’s role as a catalyst

Question 6

Energy

Answer 6

the ability to do work

Question 7

Enzyme

Answer 7

Enzymes are proteins that act as biological catalysts by accelerating chemical reactions, resulting in an increased rate of chemical reaction.

Question 8

Enzyme denaturation

Answer 8

Breaking of enzymes chemical bonds altering its 3-dimensional shape.

Question 9

Enzyme inhibitor

Answer 9

renders the activation site unavailable without damaging the enzyme.

Question 10

Enzyme Saturation

Answer 10

a situation whereby the substrate which the enzymes help react is at such a high concentration that the enzyme molecules are always binding to it. Substrate is at max concentration.

Question 11

Induced fit

Answer 11

model proposing that the binding of a substrate or some other molecule to an enzyme causes a change in the shape of the enzyme so as to enhance or inhibit its activity

Question 12

Metabolic pathway

Answer 12

a series of connected chemical reactions that feed one another

Question 13

Metabolism (definition and function)

Answer 13

Sum total of all chemical reactions occurring within an organism. Manages the material and energy resources of the cell. Function is to gather energy and reproduce.

Question 14

protein

Answer 14

a naturally occurring, extremely complex substance that consists of amino acid residues joined by peptide bonds

Question 15

Substrate specificity

Answer 15

The preference of an enzyme for one specific substrate

Question 16

Compaire and contrast cofactors and coenzymes

Answer 16

All coenzymes are cofactors. Coenzymes are organic cofactors.

Question 17

What is the general function of an organism’s metabolism?

Answer 17

Manages the material and energy resources of the cell, ultimate function is to gather energy and reproduce the organism.

Question 18

Describe at least three enzyme-catalyzed reactions that occur in your body. How important do you think each is to your continued existence?

Answer 18

ATPsynthase catalyzes the addition of a 3rd phosphate group to make ATP

Sucrase breaks down sucrose into monosaccharides

DNA ligase covalently links two DNA molecules

Question 19

What is a metabolic pathway? Does a single enzyme catalyze all of the steps of a given metabolic pathway? Explain.

Answer 19

Series of chemical reactions converting a starting molecule into an end product. No, multiple enzymes can be used or a single enzyme can be used depending on the pathway.

Question 20

Are all enzymes proteins? Are all proteins enzymes? Explain.

Answer 20

Yes all enzymes are proteins but not all proteins are enzymes.

Question 21

Are all enzymes catalysts? Are all catalysts proteins? Explain.

Answer 21

Yes all enzymes are catalysts but not all catalysts are proteins since not all catalysts are enzymes.

Question 22

If a particular chemical reaction would occur even in the absence of an enzyme, do you think the presence of an enzyme might still be important? Explain.

Answer 22

Yes, enzymes increase the rate of the reaction. Sure the reaction would occur anyway but not in a timely enough manner to keep the organism moving and functioning. Enzymes help the reactions keep up with the needs of the organism.

Question 23

Given your understanding of enzyme names, what would be a general term for a type of enzyme that is able to break down (hydrolyze) proteins into their constituent amino acids?

Answer 23

Proteases

Question 24

Enzyme naming

Answer 24

Name ends with suffix -ase, name of the enzyme substrate is incorporated. Sucrase-breaks down sucrose, lactase-breaks down lacrosse, and DNA ligase- covalently links DNA molecules.

Question 25

Given your understanding of enzyme names, what would be a general term for a type of enzyme that is able to assemble nucleotides into DNA molecules?

Answer 25

DNAse

Question 26

How does energy relate to the breaking and to the formation of chemical bonds during a chemical reaction?

Answer 26

Breaking bonds requires energy while forming new bonds releases energy. Sometimes there’s a net release, sometimes there’s a net requirement. Net requirement you spend more energy than you make while net release you gain a net growth in energy.

Question 27

Describe an exergonic reaction in terms of the potential energy of its reactants and the potential energy of its products. Now include the concept of activation energy and describe the potential energy of the “transition state.” How would an enzyme impact such a reaction?

Answer 27

In an exergonic reaction the free energy of the reactants is higher than the products. Thus there is a net release of energy. The activation energy is the “hump” required for the reaction to proceed.

Question 28

Describe an endergonic reaction in terms of the potential energy of its reactants and the potential energy of its products. Now include the concept of activation energy and describe the potential energy of the “transition state.” How would an enzyme impact such a reaction?

Answer 28

Reactants have a lower free energy than the products. Little energy is released, most of it withheld in the products. The net released energy is the difference between the activation energy and the product energy. The activation energy is closer to the products than the reactants.

Question 29

Is striking a match an exergonic reaction? Why doesn’t a match spontaneously combust in your pocketses? (Gollum helped write this question…)

Answer 29

Yes, it’s exergonic. An initial input of energy is required, which supplies the activation energy (striking the match). The result is a great deal of released energy, greater than the input.

Question 30

If a net release of energy accompanies the breakdown of DNA, why is your genetic material inherently stable?

Answer 30

They are stable because the activation energy required for their decomposition are rarely reached.

Question 31

Spontaneously

Answer 31

net release of energy, spontaneous formation of products. Activation energy still applies.

Question 32

There is a net release of energy during the conversion of ATP into ADP. What chemical bonds are broken during this process? Is energy required or is it released in this breaking process? What new chemical bonds are formed during this process? Is energy required or is it released during this bond formation process?

Answer 32

ATP + H20, results in two bonds breaking which requires input of energy. The reforming of the new bonds H to the one phosphate and OH to another results in a huge release of energy greater then the input of energy. Resulting in a net release of energy.

Question 33

There is a net requirement for energy during the conversion of ADP into ATP. What chemical bonds are broken during this process? Is energy required or is it released in this breaking process? What new chemical bonds are formed during this process? Is energy required or is it released during this bond formation process?

Answer 33

ADP+P+energy, breaking bonds H from ADP and OH from P. This requires the input of a large amount of energy. Forming new bonds between ADP and P releases a little energy. Result is a net input of energy so endergonic reaction.

Question 34

Why is it important that living organisms have so many different enzymes?

Answer 34

Because enzymes are reaction specific and there are a lot of reactions in living organisms.

Question 35

All humans can hydrolyze the sugar sucrose, but only some humans can hydrolyze the sugar lactose, and no humans can hydrolyze the polysaccharide cellulose. Explain the basis for these differences.

Answer 35

“substrate specificity”, enzymes are specific to the reaction they are able to catalyze. The enzyme that works on sucrose is not the same that works on lactose which is not the same as the on that works on cellulose.

Question 36

Describe the relationship between an enzyme and its substrate, including the concept of induced fit.

Answer 36

The activation site on the enzyme is specific to the substrate. Only certain substrates will fit into the specific enzyme. “induced fit” like shaking hands. The shape of the enzyme will alter slightly after contact, becoming and even better fit for the substrate.

Question 37

The precursor metabolite phosphoenolpyruvate (PEP) can be acted upon by several different enzymes and converted into several different molecules. Explain how this is consistent with the concept of substrate specificity.

Answer 37

Single substrate may be acted upon by multiple enzymes. All of the enzymes have an active site specific to the PEP, the reaction that occurs between the enzymes spitting out different products.

Question 38

Does the presence or absence of an enzyme affect whether a given chemical reaction is endergonic or exergonic? Explain.

Answer 38

No. Enzymes do not change the reactant or product energy; it lowers the activation energy. Lowers the amount of input energy needed, lowers the hump to reach products. Net change in free energy remains unchanged.

Question 39

List and explain the steps in the catalytic cycle of an enzyme.

Answer 39

Reactants are called substrates and within the enzyme is activation site. The mouth is the active site and the substrates fit into this activate site held in with weak bonds (like hydrogen bonds). Bonds are broken and reformed between the reactions within the activated site via a route of lowered activation energy. Enzyme then spits out the products opening the activation site for more substrate.

Question 40

What is the general means by which an enzyme increases the rate of a chemical reaction?

Answer 40

lowering activation energy.

Question 41

Though it is quite variable between enzymes, describe the general rate of an enzyme-catalyzed reaction.

Answer 41

1000 substrate molecules per second.

Question 42

List at least six different factors that can affect the rate of an enzyme-catalyzed reaction.

Answer 42

Substrate concentration, enzyme concentration, temp, pH, cofactor availability, and inhibitors.

Question 43

Does adding more enzyme sometimes speed up the rate of an enzyme-catalyzed reaction? Does it always? Explain, including the concept of enzyme saturation in your discussion.

Answer 43

If substrate concentration is reasonably high and enzyme concentration is low then increasing enzyme concentration will speed up the rate of reaction. However, the limiting factor is now the substrate. These enzymes can only move as fast as there is substrate available otherwise they are exiting with empty active sites.

Question 44

Does adding more substrate sometimes speed up the rate of an enzyme-catalyzed reaction? Does it always? Explain.

Answer 44

Increasing substrate concentration may or may not speed up the rate of reaction. If it is very low, an increased rate is seen but if it’s already high no change occurs. Enzymes need to bump into the substrates so more is nice, however there is a point where the enzyme is “saturated”. This occurs when all the enzyme active sites are full, the rate that the enzyme functions at is the limiting factor for how quickly it can take in more substrate.

Question 45

Describe the phenomenon of protein denaturation, giving at least one specific example of this process.

Answer 45

Enzymes have specific 2 dimensional structures held together by chemical bonds (covalent, ionic, and hydrogen bonds). Breaking these bonds denature the enzyme altering the 3-dimensional shape. Enzymes cease to function, often irreversible. Can be caused by temp and or pH changes. Cooking an egg on the stove denatures the proteins with the egg causing it to go from a viscous structure to a solid structure.

Question 46

How does temperature typically affect the rate of a chemical reaction that is not catalyzed by an enzyme?

Answer 46

Generally increases the rate of a chemical reaction. Substrates collide more frequently.

Question 47

How and in why does temperature affect the rate of an enzyme-catalyzed reaction?

Answer 47

Increased temperature breaks the bonds within the enzyme (protein) changing the bonds and denaturing it. Resulting enzymes display a bell curve. Decreasing temperature decreases the rate of reaction enzymes are not able to modify shape as well to fit substrates.

Question 48

At what temperature do most human enzymes display maximal activity? Why is this the case?

Answer 48

37 C, because is that normal body temp for which they are designed to function.

Question 49

Thermus aquaticus is a bacterium that lives in hot springs. How would you expect the activity its enzymes compare to the activity of human enzymes? Explain.

Question 50

How would you expect the activity of an alligator’s enzymes to compare to the activity of human enzymes? Explain.

Answer 50

Normal temp is about 37 C but body temp is less constant, reliant on environment.

Question 51

How and why does pH affect the rate of an enzyme-catalyzed reaction?

Answer 51

pH disrupts the ionic and hydrogen bonds. pH measures the reactive abundance of H+ ions and OH- ions. Acidic pH increases the H+ ions whill then compete for the legative bindings that make up the enzyme. Basic pH increases number OH- ions and they compete for the + charges within the enzyme.

Question 52

Describe, in terms of enzymes, how pasteurization and subsequent refrigeration of milk suppresses unwanted bacterial growth.

Answer 52

Growth of unwanted bacteria can be controlled by denaturing their protein. This is how pasteurization works. Vinegar does the same thing by changing the pH and ammonia does the same thing to kill certain bacteria in pickeling.

Question 53

How does a cofactor relate to the function of an enzyme?

Answer 53

cofactors empower enzymes to function at maximal catalytic effectiveness or endurance.

Coenymes consist entirely of one or more polypeptide. Someposses both proteins and non-protein. Non-protein term is a cofactor, protein portion is apoenzyme.

Question 54

Give at least three examples of inorganic cofactors. Under what category might these be listed within the nutritional information on your cereal box?

Answer 54

Fe2+, Mg+2, Cu 2+

Question 55

Give at least three examples of organic cofactors. Under what category might these be listed within the nutritional information on your cereal box?

Answer 55

Vitamins A B C

Question 56

Describe a process by which DNA-degrading enzymes are commonly inactivated during a DNA isolation procedure.

Answer 56

DNAse catalyzes the hydrolysis (destruction) of DNA. Cofactor is Mg2+ and removal of Mg2+ inactivates the enzyme. DNA isolation

Question 57

How is a competitive inhibitor like a non-competitive inhibitor? How are they different?

Answer 57

Competitive inhibitors resemble the substrate to compete for the active site, blocks substrate from entering the cell, no reaction occurs to from products. Can be competitive or reversalbe.

Non-competitive inhibition, moleuclebinds to site other than activation site called “allosteric sites”
Non competitive inhibitors do not resemble the substrate, binds to site other than the active site. Results in change of shape to the active site. Site is till open but its shape is now different and no longer fits the substrate. Increased substrate concentration cannt over come this change.

Question 58

Give at least three specific examples of practical applications involving the inhibition of enzymes.

Answer 58

Nerve gasses, inhibit the enzyme acetylchloisetersa, which is involved in communication of nerve cells and muscle cells. Cannot get energy from food.

Cyanide, irreversibly inhibits the enzyme chytochrome oxidase which is important in aerobic cellular respiration.

Penicillin, completely inhibits the bacterial enzyme transpeptidase which participates in building cell walls resulting in changes in osimoos.

Sulfa drugs competivitly inhibit a bacterial enzyme required for folic acid synthesis which is requried for dNA snythesis.

Ibuprofen inhibits enzymes involved in production of prostaglandins which are involved in inflammation and pain. Enyxme plocks production decreasing pain.

Question 59

describe the process of feedback inhibition.

Answer 59

Negative feedback or end-product inhibition. End product acts as a allosteric inhbiitor in an earlier part of the oatway. Product synthesized only when needed.

Question 60

Compare non-competitive inhibition (a.k.a. allosteric inhibition) to excitatory allosteric control. How are they similar? How are they different?

Answer 60

Excitatory allosteric control, activator molecule binds to enzymes allosteric site which alters shape of activation site. Activates otherwise inactive enzyme.

Allosteric inhibition binds to the allosteric site which alters activative site shape so substreate canoot bind.

Allosteric turns enzume off while excitatory turns enzyme on.

Question 61

What is a ribozyme?

Answer 61

Biological catalysts, composed of RNA not protein.
RNA has 3 key abilities: storage of genetic information, capacity for self relocation, ability to perform and variety of “enzymatic” functions.

Question 62

How is a ribozyme like an enzyme? How is it different?

Answer 62

Enzyme like in that it catalyzes a specific reaction. Not composed of protein like enzymes..

Question 63

The enzyme sucrase cleaves the disaccharide sucrose into the monosaccharides glucose and fructose. To which category of enzymes does sucrase belong?

Polymerase
Ligase
Hydrolase
Isomerase
Oxidoreductase

Answer 63

Hydrolase

Question 64

Which of the following is NOT important in stabilizing the three-dimensional structure of an enzyme?
1. covalent bonds between variable (“R”) groups of non-adjacent amino acids

2. hydrogen bonds
3. all of these types of bonds are important in defining the three-dimensional structure of a protein

4.covalent bonds between adjacent amino acids

5. ionic bonds

Answer 64

3. all of these types of bonds are important in defining the three-dimensional structure of a protein