chapter 3

Question 1

what are enzymes?

Answer 1

• biological catalysts
  
  • speed up the rate of a reaction by reducing the activation energy
  • sensitive to temperature and pH
  • specific for certain reactions or classes of reactions
  • do not affect the equilibrium of a reaction or the thermodynamic paramters of the reaction
  • also speed up the reverse reaction in order to avoid affecting the equilibrium

Question 2

the substance that an enzyme operates on is known as?

Answer 2

• a substrate and they interact at the active site of an enzyme, which can be divided into a binding site and a catalytic site

Question 3

what is a catalytic and binding site?

Answer 3

• the catalytic site is the very specific place where a reaction is catalyzed
• the binding site is a larger area where the substrate interacts with the enzyme through intermolecular interactions in a way that positions the substrate properly relative to the catalytic site
  
  • when the substrate interacts with the active site of an enzyme it forms the enzyme-substrate complex

Question 4

regulatory elements that interact with an enzyme at its active site are known as?

regulatory molecules that bind at some other site of an enzyme are known as?

the substance that an enzyme interacts with can be reffered to as?

Answer 4

• orthosteric
• allosteric
• ligand

Question 5

what are the 2 important models proposed to describe how enzymes interact with substrates?

Answer 5

• lock and key- proposes that the active site of an enzyme and the substrate fit together like puzzle pieces, with no change in tertiary or quaternary structure
• induced fit model- the enzyme and substrate are seen as affecting each otehr; the initial stages of binding induce conformational shifts that allow closer binding and more efficient catalysis

Question 6

what are oxidoreductases?

Answer 6

• catalyze redox reactions

Question 7

what are transferases?

Answer 7

• transfer a functional group between molecules

Question 8

what are hydrolases?

Answer 8

• catalyze hydrolysis

Question 9

what are lyases?

Answer 9

• cleave bonds through non-hydrolysis mechanisms

Question 10

what are isomerases?

Answer 10

• catalyze isomerization

Question 11

what are ligases?

Answer 11

• join moelcules together with covalent bonds

Question 12

enzymes in a metabolic pathway are commonly regulated by downstream products of the pathway, which is a process known as?

Answer 12

• feedback regulation

Question 13

what is negative feedback/feedback inhibition?

Answer 13

• the downstream product of a pathway acts to inhibit the pathway itself
  
  • when we have enough of a product, then we don’t need to produce more of it

Question 14

what is positive feedback?

Answer 14

• ex. blood clotting
  
  • positive feedback allows a quick response, while negative feedback ensures that the process doesn’t spiral out of control

Question 15

what is feed-forward regulation

Answer 15

control of a metabolic pathway by a metabolite of the pathway that acts in the same direction as the metabolic flux, i.e. downstream or ‘later’ in the pathway, e.g. the activation of pyruvate kinase by fructose 1,6-bisphosphate.

an enzyme is regualted by an upstream product of the pathway

Question 16

what is cooperativity?

Answer 16

• when an enzyme has multiple active sites and binding at one active site facilitates or makes the second binding easier or harder
  
  • positive = easier
  • negative = harder

Question 17

the degree of cooperativity in an enzyme or protein can be expressed using?

Answer 17

• the Hill coefficient
  
  • a Hill coefficint > 1 results from positive cooperativity
  • equal to 1 indicates non-cooperativity
  • < 1 negative cooperativity

Question 18

what is the Michaelis-Menten model of enzyme kinetics?

Answer 18

• The Michaelis-Menten model (1) is the one of the simplest and best-known approaches to enzyme kinetics. It takes the form of an equation relating reaction velocity to substrate concentration for a system where a substrate S binds reversibly to an enzyme E to form an enzyme-substrate complex ES, which then reacts irreversibly to generate a product P and to regenerate the free enzyme E.

Question 19

what is teh definition of Km?

Answer 19

• the concentration of substrate that corresponds to half of v_max
  
  • _​can be used as a measure of the affinity that an enzyme has for its substrate
  • Km is not affected if you change the concentration of the substrate or enzyme, but can be affected by inhibitors

Question 20

what is the Michaelis-Menten equation?

Answer 20

v = v_max[S]/Km + [S]

Question 21

what are lineweaver-Burk plots?

Answer 21

• double-reciprocal transformation of Michaelis-Menten plots

Question 22

parameters of Km abd Vmax on a linweaver burke plot?

Answer 22

• increase Km = increase in intercept (became less negative) so moved towards origin
• decrease Km = decrease in intercept (became mroe negative) so moved away from origin
• increase v_max = decrease (become less positive) so moved towards origin
• decrease v_max = increase (became more negative) so moved away from origin

Question 23

what are inhibitors?

Answer 23

• substances that reduce the effective activity of enzymes
  
  • can be reversible or irreversible

Question 24

how do non reversible inhibitors interact with enzymes?

Answer 24

• through non-covalent interactions

Question 25

what are competitive inhibitors?

Answer 25

* an inhibitor competes with substrate binding to the active site, resulting in an unchanged vmax and an increased Km

Question 26

what are noncompetitive inhibitors?

Answer 26

* a subclass of mixed inhibition in which an inhibitor binds to the enzyme alone 50% of the time and the enzyme-substrate complex 50% of the time, resulting in a decreased vmax and an unchanged Km

Question 27

what is uncompetitive inhibition?

Answer 27

* an inhibitor binds to the enzyme-substrate complex, resulting in a decreased vmax and a decreased Km

Question 28

what is mixed inhibiton?

Answer 28

* an inhibitor binds to both the enzyme alone and the enzyme-substrate complex, resulting in a decreased vmax and an increased or decreased Km * Vmax decreases and Km varies

Question 29

summary of enzyme inhibitors?

Answer 29

Question 30

enzyme inhibitors effects on MM plot?

Answer 30

Question 31

enzyme inhibitors on LWB plot?

Answer 31

Question 32

what does phosphorylation refer to?

Answer 32

* attaching a phosphate group to a protein and dephosphorylation refers to removing it * affects enzyme activity

Question 33

phosphorylation most often targets?

Answer 33

* serine, threonine, and tyrosine which all have -OH groups that a phosphate can be attached to

Question 34

what catalyses phosphorylation and what catalyses dephosphorylation?

Answer 34

* kinases * phosphatases

Question 35

what does glycosylation refer to?

Answer 35

* the modification of enzymes by carbohydrate moieties with a broad range of effects

Question 36

what are zymogens?

Answer 36

* aka proenzymes are inactive forms of enzymes that must be cleaved to become active

Question 37

what are cofactors?

Answer 37

A cofactor is a non-protein chemical that assists with a biological chemical reaction. Co-factors may be metal ions, organic compounds, or other chemicals that have helpful properties not usually found in amino acids. Some cofactors can be made inside the body, such as ATP, while others must be consumed in food (organic = coenzymes like vitamins- ex. coenzyme A which transfers acyl groups from one place to another).

Question 38

coenzymes that are tightly bonded to their enzyme are known as?

Answer 38

* prosthetic groups * ex. heme which contains an iron ion in the center of a porphyrin ring, and is attached to oxygen-transport proteins

Question 39

what is a holoenzyme?

Answer 39

* an enzyme together with the coenzyme(s) and/or metal ions it needs to carry out its catalytic activity

Question 40

what is an apoenzyme?

Answer 40

* refers to an enzyme without the coenzymes/cofactors it needs to function correctly