Lect 9. Energy & Metabolism - Enzymes

Question 1

What is an enzyme?

Answer 1

A catalyst or catalytic protein that speeds up the rate of a reaction without being consumed or altered by the reaction.

W/out enzymes, the pathways of metabolism would be too slow to maintain an organism’s biological needs

Question 2

What is the state in which the reshaping of the starting molecule into a highly unstable state is involved?

Answer 2

the transition state

this happens before the reaction can proceed

Question 3

The energy needed to reshape the reactant molecule is called:

Answer 3

the free energy of activation / activation energy Ea

Question 4

Ea is often supplied in which form?

Answer 4

It is often supplied in the form of heat that the reactant molecules absorb from their surroundings. This thermal E increases the speed of the molecules, making them collide more and harder causing the bonds to break.

Question 5

Ea provides a barrier that determines:

Answer 5

the rate at which a reaction will occur.

Question 6

Heat speeds up a reaction by allowing reactants to reach the transition state more often. But why is using thermal energy inappropriate for biological systems?

Answer 6

• High temp denatures proteins and kills cells
• Heat would speed all the cells reactions, not just the necessary ones

Question 7

Enzymes are very selective in the reactions they catalyze: they determine which chemical reaction will occur, when and where in the cell. What is the location on the enzyme at which the reaction occurs called? (Where does the substrate bind on the enzyme?)

Answer 7

Active Site

Question 8

Enzyme + substrate(s) =

Answer 8

enzyme-substrate complex (temporary)

When enzyme and substrate join, catalytic action of enzyme converts S to product

Question 9

Most metabolic reactions are reversible: an enzyme can catalyze both _____.

Answer 9

forward and reverse reactions

Question 10

The capacity of an enzyme to catalyze both reactions depends on:

Answer 10

the concentration of both substrate and products

Question 11

An active site is typically:

describe it

Answer 11

a pocket or groove on the surface of the protein formed by a few AAs

Question 12

Substrate is held in active site mainly by:

bonding?

Answer 12

H-bonds and some ionic bonds

Question 13

Interaction b/w substrate and the AAs of the protein cause the active site to fit more snuggly around the substrate. This is called:

Answer 13

induced fit

It brings chemical groups into position that increase chemical reaction rate.
The product leaves the active site and a new substrate enters.

Question 14

How do enzymes lower the Ea? (4)

Answer 14

1. provide template for substrates to come together in proper orientation (otherwise rely on random molecular motion)
2. can stretch the substrate molecules toward transition state (bending and stressing critical bonds)
3. can directly participate in the chemical reaction (often involves brief covalent bonding between an active site R-gr and the substrate)
4. can provide a favourable microenvironment that is more conductive to a particular type of reaction (ex: active site composed of AA.s w/ acidic R-gr creates a pocket of low pH in neutral cell)

Question 15

The rate at which an enzyme converts a substrate to a product depends on:

Answer 15

initial substrate concentration. The greater the [ ] of S molecules, the more frequently they come in contact w/ enzyme’s active site.

Question 16

At a certain concentration, all active sites are taken up. This is the substrate concentration at which the enzyme is:

Answer 16

saturated.

Question 17

At enzyme saturation, the rate of the reaction depends on:

Answer 17

how fast the active site can convert the substrate to product.

The cell can speed up the reaction rate by adding more enzyme molecules.

Question 18

Optimal Enzymatic Conditions

Temperature: up to a point, the rate of an enzymatic reaction increases with an increase in temp, because:

Answer 18

there is an increase in collision of substrate molecules with enzyme molecules.

Question 19

Most enzymes have an optimal pH ranging from

Answer 19

6 to 8

Question 20

Optimal temperature and pH of an enzyme will vary on type of organism it is found in and where in the organism it is found. ex: lysosomes have a ____ pH

Answer 20

low pH. HCl help denature 4°, 3° and even 2° proteins.

Question 21

Co-factors

Various types of chemicals can serve to promote or inhibit enzyme activity. Prosthetic groups or co-enzymes are:

Answer 21

inorganic or organic molecules that allow the enzyme to function properly. They can be bound tightly to the enzyme or they can bind loosely and reversibly.

Question 22

A holoenzyme consists of:

Answer 22

1. aa (protein) part of the enzyme called apoenzyme
2. non-protein part called the cofactor

Question 23

Terminology Summary

Simple Protein: made only aa
Conjugated Protein is also called:

Answer 23

holoenzyme

Question 24

The aa part of a holoenzyme is called

Answer 24

the apoenzyme

Question 25

If the cofactor of a holoenzyme is organic, it is a

Answer 25

co-enzyme

most vitamins

Question 26

If the co-factor of a holoenzyme is inorganic, it is called a

Answer 26

prosthetic group

ex: zinc, copper, iron, magnesium

Question 27

Regulating Enzyme Activity

In order to have a properly functioning cell, it must be able to tightly regulate its metabolic pathways. This is done, in part, by controlling when and where an enzyme is active. Achieved in 2 ways:

Answer 27

1. switching on or off the genes that encode specific enzymes (gene regulation)
2. regulating the activity of an enzyme once it has been synthesized (inactive enzyme when w/out an effector in allosteric site)

Question 28

Once the enzyme has been synthesized, there are 2 ways to regulate its activity:

Answer 28

1. Activation or Inhibition
2. Feedback Inhibition

Question 29

Often, molecules that regulate enzyme activity do so by acting like noncompetitve reversible inhibitors or activators. These reversibly bind to allosteric sites and either stabilize an enzyme in its active form (____) or deactivate it (____).

Answer 29

These reversibly bind to allosteric sites and either stabilize an enzyme in its active form (activators) or deactivate it (inhibitors).

Question 30

An enzyme inhibitor is

Answer 30

any molecule that prevents an enzyme from functioning properly (inhibits catalysis).

ex: Penicillin blocks the active site of an enzyme used in the synthesis of bacterial cell walls

Question 31

Inhibition of an enzyme activity can be irreversible if the inhibitor binds to the enzyme:

Answer 31

covalently.

Question 32

Inhibition of an enzyme activity can be reversible if the inhibitor binds to the enzyme:

Answer 32

with weak bonds.

Question 33

Differentiate competitive and noncompetitive inhibitors

Answer 33

competitive:
- resemble normal substrate of enzyme
- compete with substrate for the active site
noncompetitive aka allosteric inhibitors:
- do not directly compete with substrate for active site
- instead bind to the enzyme at another location (allosteric site)
- causes enzyme to change shape -> active site less effective

Question 34

How can the competition between (competitive) inhibitors and substrate be overcome?

Answer 34

by increasing substrate concentration

Question 35

Cooperativity is another form of:

Answer 35

allosteric activation

Question 36

The binding of one substrate molecule to 1 active site may affect the other ones in the complex. One substrate molecule primes the enzyme to:

Answer 36

accept additional substrate molecules. It stimulates catalytic activity of the enzyme.

Question 37

In feedback inhibition, a pathway is shut off by its own end-product. The end-product becomes the ____ to an enzyme that acts early in the pathway.

common method of metabolic control

Answer 37

The end-product becomes the inhibitor to an enzyme that acts early in the pathway.

ex: ATP can allosterically inhibit an enzyme involved in the ATP-generating pathway.