lecture 3: enzymes

Question 1

what is metabolism?

Answer 1

thousands of chemical reactions linked through metabolic pathways

Question 2

what are reactions catalyzed by?

Answer 2

enzymes

Question 3

what are enzymes?

Answer 3

biological catalysts

Question 4

what do catalysts do?

Answer 4

speed up reaction by lowering activation energy

Question 5

do spontaneous reactions need enzymes? why is this good for our body?

Answer 5

yes they do. it is good in our body, because we dont want these reactions happening at random times in our body. they regulate the reactions in our body.

Question 6

what is activation energy?

Answer 6

initial input of energy required to break bonds in reactants and allow them to form products. amount of energy required for reactants to reach the transition state

Question 7

true or false? in a spontaneous reaction the potential energy of products is higher than reactants.

Answer 7

false! in a spontaneous reaction, the potential energy of the products is lower than the potential energy of the reactants.

Question 8

how does lowering activation energy catalyze a reaction?

Answer 8

it increases the number of molecules that have enough energy to react.

Question 9

what is the transition state?

Answer 9

an in-between state when old bonds are being broken so that new bonds can be formed.

Question 10

physically, how do enzymes help with reactions?

Answer 10

they grab onto reactants and bring them together with the right orientation.

Question 11

do enzymes change delta G?

Answer 11

NOOOOOO

Question 12

how do enzymes regulate reactions?

Answer 12

-enzymes for certain reactions are not created if not needed
-use phosphate group to change their shape which changes function (phosphorylation)

Question 13

what is another word for reactants?

Answer 13

substrate

Question 14

what do we mean by enzymes are substrate specific?

Answer 14

only bind to specific substrates

Question 15

What does the reaction with an enzyme form?

Answer 15

Question 16

what is the active site?

Answer 16

pocket or groove on the protein’s surface where the substrate binds

Question 17

through which bonds does the substrate bind to the enzyme’s active site?

Answer 17

non-covalent interactions such as H-bonds and ionic bonds

Question 18

are ionic bonds considered weak or strong in bio?

Answer 18

weak, cause you dont need enzymes to break them

Question 19

what does the induced fit of an enzyme mean?

Answer 19

binding of substrate causes a change in the shape of the enzyme to bring amino acid side chains in position to catalyze the reaction

Question 20

how do enzymes lower activation energy?

Answer 20

1) holding substrates in the correct orientation and+ close together for reaction to occur
2) stressing bonds in substrates (s) so that they are easier to break
3) create a micro-environment in the active site (ex: PH, can favour reaction by making active site basic or basic)
4) enzyme can be directly involved in reaction (the amino acid chains in active site are acting like reactants)

Question 21

factors that affect reaction rate?

Answer 21

1) substrate concentration
2) enzyme concentration
3) environmental conditions (temperature, PH)
4) cofactors or coenzymes

Question 22

What does increasing substrate concentration do to reaction rates?

Answer 22

Reaction rates increase until point of saturation cause there are no more active sites that can be used. it increases the chance of the enzyme and substrate finding each other

Question 23

What does increasing enzyme concentration do to the reaction rate?

Answer 23

Increases rate of reaction

Question 24

how does temperature affect reaction rates?

Answer 24

1) increasing temperature increases the frequency of collisions between substrates and active sites, therefore increasing reaction rate.

2) after a certain heat, reaction rate goes dow, as excess temperature denatures the enzymes

Question 25

What would an increasing enzyme graph look like if we didn’t have an excess amount of substrate?

Answer 25

Question 26

What does the graph of temperature increase vs reaction rate look like?

Answer 26

Question 27

how does PH affect reaction rates?

Answer 27

enzymes are usually most active within a specific pH range. extreme pHs affect the ionization of amino acid side chains and causes the enzyme to denature.

Question 28

what does the pH vs rate of reaction graph look like?

Answer 28

Question 29

what are cofactor and coenzymes?

Answer 29

non-protein molecules that can bind permanently or reversibly to the enzyme. they help the enzymes

Question 30

what’s the difference between cofactors and coenzymes?

Answer 30

-cofactors: inorganic metal ions

-coenzymes: organic molecules (ex: vitamins)
-bind weakly to enzyme
ex: NAD+, FAD coenzyme A

Question 31

what type of enzyme inhibition exists?

Answer 31

irreversible and reversible

Question 32

what is irreversible inhibition? give examples

Answer 32

-not good
-inhibitor attaches by a covalent bond (nerve gas, penicillin, some poisons)

Question 33

what is reversible inhibition? give an example

Answer 33

-inhibitor attaches by weak, non-covalent bonds
-important part of regulating metabolism in our body
-example:ATP inhibits PFK enzyme

Question 34

why are irreversible inhibitors not found in our bodies?

Answer 34

because the reactions in our body happen for a reason. they need to be regulated. enzymes need to be turned on and turned off

Question 35

other than reversible and irreversible, what else can enzyme inhibitors be?

Answer 35

competitive/non-competitive

Question 36

what are competitive inhibitors?

Answer 36

-inhibitor binds to active site and competes with substrates for binding
-can be overcome by increasing substrate concentration (more likely that the substrate will bond to enzyme instead of inhibitor because more substrate. mimics the substrate, competing for the active site

Question 37

what are non-competitive inhibitors?

Answer 37

-inhibitor binds somewhere else on the enzyme (not the active site)
-causes enzyme to change shape so that it can no longer bind to substrate
-increasing substrate concentration does not overcome inhibition (enzyme cant bind to substrate anyways, because the change of its shape)

Question 38

in which reaction has the competitive/non-competitive inhibitor been added?

Question 39

what are allosteric enzymes?

Answer 39

-involved in regulation of metabolic pathways
-comprised of more than one polypeptide (each with own active site)
-special type of enzyme

Question 40

what do enzyme inhibitors do?

Answer 40

they turn enzymes off

Question 41

what are allosteric enzyme regulators?

Answer 41

-molecules that bind weakly to allosteric site
-can be inhibitor or activator of the enzyme

Question 42

what is the difference between allosteric activators and inhibitors?

Answer 42

-inhibitors: stabilize the active form of the enzyme
-inhibitors: stabilize the inactive form of the enzyme

inhibitors and activators often compete for the allosteric site

Question 43

what is negative feedback inhibition/feedback inhibition?

Answer 43

negative feedback inhibition happens when something near the end of a metabolic pathway inhibits the enzyme of a reaction early on in the pathway.

Question 44

why does negative feedback inhibition make sense for regulation?

Answer 44

products shut down their own production when there’s enough. it prevents the wasting of cell resources. dont even need any external help.

Question 45

how does allosteric regulation apply to ATP?

Answer 45

-ATP acts as an allosteric inhibitor of PFK
-AMP acts as an allosteric activator of PFK