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Flashcards in Enzyme Kinetics Deck (44):
1

Define: Catalyst

Increases the rate of reaction by decreasing the energy barrier

2

Why are enzymes a special type of catalyst?

  1. They can increase the rate by 106 to 1012 greater than non-catalyst reactions, and 103 increase greater than non-enzymatic catalysts.
  2. Can occur in mild conditions (pH 7, >100C°, 1atm)
  3. Can be regulated by biologcial molecules

3

Unit (when measuring ezymic activity)

Amount of substrate converted to product in a given time (ex: 1µmol/min)

4

Specific Activity

Number of units per a mg of protein

5

Temperature optimum: definition and average for humans

The temperature at which ezymes perform the best. Typically 37C° for humans

6

pH optimum for pepsin

pH of 2

7

pH optimum of Trypsin

pH of 8

8

Oxidoreductases

Catalyze reduction-oxidation reactions

9

Transferases

Catalyses the transfer of a group (glycosyl, methyl, phosporyl)

10

Hydrolases

Catalyzes hydrolytic cleavage of bonds

(C-C, C-O, C-N, and others)

11

Lyases

Catayzes atom elimination to leave double bonds 

(C-C, C-O, C-N, and others)

12

Isomerases

Catalyses geometric/structural changes in a molecule

13

Ligases

Catalyzes the joining of 2 molecules.

Coupled to hydrolysis of ATP

14

Active Site

Specific region on the enzyme where the catalysis occurs. Substrates bind to the active site (plus any required elements) in a specific manor. Enzyme structure determines active site structure, so changes in structure may (or may not) affects the active site.

15

Catalysis by proximity

Molecules must come within bond forming distance. Active sites create a high local concentration of the target molcule by binding it. Substrates are bound in a specific orientation conducive to the reaction.

16

Acid-Base Catalysis

Ionizable functional groups of amino acids may act as an acid or base in the catalysis

17

Catalysis by strain

If catalyzing reaction is to break bonds, the substrates may be bound in such a way that the bonds are destabilized.

18

Covalent Catalysis

The enzyme and substrate covalently bond. The modified enzyme becomes the subtrate for a different reaction. 

Keq of the modified enzyme > Keq of the inital substrate to the product

19

Prostetic groups

Tightly/stably incorporated into the proteins (sometimes by covalent bonds). Metal ions are the most common.

20

Most common metal prostetic groups

Co, Cu, Mg, Mn, Zn

21

Cofactors

Bind transiently to the substrate or enzyme, but are required for activity

22

Metalloenzymes

Enzymes that contain a metal prostetic group

23

Coenzymes

Accept a group from one reaction, and supplies groups in other reactions

Ex: CoA transfers acyl groups, Folates transfer 1 carbon groups

24

Isoenzymes

Physically different enzymes that catalyze the same reaction. May have different properties like substrate affinities or activity regulation. May be expressed differently by different tissues.

25

Michaelis-Menten equation

Vmax is maximum reaction velocity

Km is the substrate concentration when v= 1/2 Vmax

When [S] = Km, v=1/2 Vmax

A image thumb
26

Significance of the slope, y and x intercept of the Kineweaver-Burk plot

Slope—Km/Vmax

Y-intercept — 1/Vmax

X-Intercept — -1/Km

27

Competitive Inhibition

Inhibitor competes with the substrate for the active site of the enzyme. Inhibitor is usually structurally similar to the substrate and only binds to the free enzyme.

28

What value do competetive inhibitors increase?

Km is increased due to the decrease in available enzymes

Vmax is unaffected because inhibitors can be overcome by the substrates

29

Noncompetitive inhibition

Bind to either the E or ES in a place other than the active site. Heavy metals act via this inhibition.

30

What values do noncompetitive inhibitors affect?

Vmax is affects because the inhibitor cannot be displaced by substrates

Km is unaffected 

31

Uncompetitive inhibition

Only binds to the ES

32

What values do uncompetitive inhibitiors affect?

Km and Vmax are both affects, creating a parallel line in the Lineweaver-Burk plot

33

When are the top and bottom equations used to calculate Ki?

Q image thumb

Vappmax is used to calculated the Ki of noncompetitive and uncompetitive enzymes

Kappm is used to calculate the Ki of uncompetitive enzymes

34

Allosteric Enzymes

The binding of one molecule facilitiates the binding of subsequent molecules to the enzyme. 

If enzyme has positive cooperativity, will respond quickly to a low amount of S. Binding of S promotes an active conformation

35

What is the Hill equation used for?

To describe the kinetics of allosteric enzymes

36

Homotropic regulation

Binding of S to allosteric enzyme increases the affinity of other catalytic sites for S

37

Heterotropic regulation

Regulatory molecule distinct from the substrate that bonds to a site other than the catalytic sites. Can be positive or negative

38

V-system effectors

Effectors that affect the catalytic rate, thus influencing Vmax 

39

K-system effectors

Effectors that affect the bonding of the substrate, thus influencing K0.5. Can be positive or negative.

40

Compartmentalization

Conflicting metabolic pathways are restricted to specific organelles to keep everything physically separate

41

Allosteric regulation

Hormones produce second messengers which are allosteric effectors of various enzymes.

Ex: hormones stimulate cAMP production and increase cytosolic [Ca2+] that interacts with calmodulin

42

Phosphorylation

Enzymes are affected by phophorylation via a protein kinase (can be specific or general)

43

Proteolytic activation

Some enzymes are synthesized in an inactive form that must be activated via a proteolytic cleavage. (Digestion and coagulation)

44

Name the 3 positive regulators of glycogen phophorylase given in class

  1. AMP (allosteric effector)
  2. Phophorylation
  3. Ca2+-calmodulin (Allosteric regulation)