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Flashcards in Enzymes and Isoenzymes Deck (80):
1

Sir Archibald Edward Garrod

First to make a connection between disease and fundamental errors of biochemical reactions

coined term "inborn errors of metabolism"


2

Mass action

La Chatelier's principle

you can alter one side by adding or removing agents from the products or reactants side to push the RXN in the opposite direction

3

Physiological acids

beta-hydroxybuteric acid
acetone
acetoacetic acid

4

Physiological bases

bicarbonate
NH3

5

There are two things enzymes DO and at least one thing

They lower the energy of activation required to transform a substrate into an activated intermediate form, and they speed up the velocity of the rxn by doing so

they do not alter gibbs free energy or substrate concentrations

6

Oxidoreductases

enzyme that transfers electrons from a donor (reducing agent) to a acceptor (oxidizing agent)

7

Transferases

transfer a functional group between molecules

8

Isomerases

rearrange/isomerize molecules

9

Lyases

add or remove atoms to a double bond or form a double bond

"synthases"

10

Ligases

"synthetases"

form bonds with hydrolysis of ATP

C-O
C-S
C-N
C-C

11

Hydrolases

cleave bonds via addition of water

12

Active Site

contains a unique microenvironment usually void of water and controls the proper shape, pH, and polarity for substrte binding and chemical reactivity

shape, pH, polarity controlled
void of water

defines microenvironment

13

Chymotrypsin

serine protease

USES serine to cleave proteins, not cleaving proteins AT serine

catalytic triad
three chains
two intra and two inter-strand disulfide linkages

catalytic triad converts serine 195 into a potent nucleophile

14

Mechanism of peptide hydrolysis

you have interacting amino acids that can stabilize, alter, and the rejuvenate one another while interacting with the peptide bonds on a protein

15

cofactors

small molecules that contribute to the chmeical reaction of the enzyme

many different roles in catalysis

16

enzymes that use the same cofactors

share the same mechanism of catalysis

17

nomenclature of cofactors '

apoenzyme vs haloenzyme

apoenzyme

enzyme without its cofactor

haloenzyme

cofactor bound and catalytically active

18

metal cofactors are

positively charged
stable coordination of active site groups
contribute to chemical reactivity

example:

ZINC activates H2O to form OH- nucleophile

19

metal cofactors (metals)

Cu, Fe, Mg, Se, Zn

20

Coenzymes

small organic molecules often derived from vitamins
bound tightly, called prosthetic group

21

Cofactor, vitamin, chemical group transferred

Thiamine pyrophosphate

from Vitamin B1

transfers 2 carbon groups

22

Cofactor, vitamin, chemical group transferred

pyridoxal phosphate

pyridoxine (vit B6)

transfers amino and carbonyl groups

23

Cofactor, vitamin, chemical group transferred

methylcobalamin

comes from B12

transfers acyl groups

24

Cofactor, vitamin, chemical group transferred

coenzyme A

panthothenic acid

vit B5

chemical groups transferred: acetyl groups

25

Cofactor, vitamin, chemical group transferred

menaquinone

from vitamin K
transfers carbonyl group and electrons

26

Cofactor, vitamin, chemical group transferred

flavin mononucleotide

riboflavin B2

transfers electrons

27

Cofactor, vitamin, chemical group transferred

NAD and NADP

from niacin (B3)

transfers electrons

28

lipoamide

from lipoic acid

transfers electrons, acyl groups

29

biotin

from biotin vit

transfers CO2

30

tetrahydrofolic acid

from vitamin B9 (folic acid)

transfers methyl groups and formyl groups

31

coenzyme F420

riboflavin B2

transfers electrons

32

B1

produces thiamine pyrophosphate

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B2

also called riboflavin

produces coenzyme F420

34

B3

also called niacin

produces NAD NADP

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B5

also called panthothenic acid

produces Coenzyme A

36

B6

also called pyridoxine

produces pyridoxal phosphate

37

B9

folic acid

produces tetrahydrofolic acid

38

B12

produces methylcobalamin

39

Ascorbic acid

comes from VC, transfers electrons

VC produces lysyl hydroxylase

40

Scurvy

vitamin C deficiency (lysyl hydroxylase)

decreased collagen assembly

41

Ariboflavinosis

riboflavin B2 required for FAD synthesis
reduced GLUTATHIONE REDUCTASE activity, requires FAD
lesions in corner of mouth and on lips, UV sensitivity

42

dehydrogenases bind

NAD+'s

43

cofactors vs coenzymes

cofactors are metal ions that associate with protein enzymes via noncovalent interactions

coenzymes

small organic molecules mostly derived from vitamins

44

cosubstrate

coenzymes that associate with enzyme temporarily. they bind in one state and detach in another. example: NAD

45

prosthetic group

coenzymes associate permanently with enzymes

include flavin adenin dinucloetide (FAD), flavin mononucecleotide (FMN) and heme

46

reductase

transfers electrons or hydrogen

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oxidase

accepts electrons or hydrogen

48

alcohol dehydrogenase

ADH

converts alcohols to aldehydes or ketones with the reduction of NAD (cofactor) to NADH

49

what is critically needed for transferase reactions

example

a third molecule to donate a group to transfer (ATP for P for example)

kinase receptors is the example

50

kinase receptors

transferases

phosphorylate themselves and others

usually transfer Ps from ATP to serine, threonine and tyrosine on another protein or themselves

51

how do hydrolases works?

they transfer functional groups to water and thereby break covalent bonds

52

Disaccharidases

hydrolases

disaccharidases cleave double sugars to single sugars

defect in LACTASE leads to lactose intolerance

53

Lyases

enzyme that catalyzes addition or removal of groups to form double bonds

54

Lyases: example of rxn and enzyme

Fructose 1,6, bisphosphate --->
Dihydroxyacetone (DHAP) + Glyceraldehyde-3-GAP (GAP)

second step of glycolysis ^

rxn is catalyzed by an ALDOLASE

55

isomerase

enzyme that catalyzes isomerization i.e. intramolecular group transfer, product is just an isomer of the substrate

56

transition state

intermediate structure that is not the substrate and not yet the product

unstable and highest free energy

57

michaelis-mentin formula

velocity of enzyme = ((Vmax)(Substrate))/((Km+(substrate))

58

x intercept of lineweaver-burke graph

-1 / Km

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y intercept of lineweaver burk graph

1 / Vmax

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slope of lineweaver burk graph

Km/Vmax

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V0 = Vmax (s) / [(s) + (km)]: this equation tells us that

when s = km, then V0 = vmax/2

62

when vmax/2, then V0 =

Vmax/2 = V0

V0 = Vmax (s)/((s)(km))

63

how to calculate Km and Vmax

reciprocal of michaelis menton

1/V0 = (km)/(Vmax)((s)) + 1/ Vmax

64

-1/km =

x intercept on lineweaver burke plot

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1/vmax =

y intercept on the lineweaver burke plot

66

Competitive -- Noncompetitive -- Uncompetitive Inhibitors

Competitive inhibitors bind and compete with the substrate for the active site of an enzyme. CI's increase the Km

Uncompetitive inhibitors bind to the enzyme-substrate complex at an allosteric site (meaning they dont prevent ES formation). UI's alter bother Km and Vm

Noncompetitive inhibitors bind either the enzyme or the enzyme-substrate complex. Affects only the Vmax.

67

Reversible Inhibitors

use what kind of bonds

hydrogen bonds, hydrophobic bonds, ionic bonds, all non-covalent bonds : bind to the enzyme but do not undergo any chemical reactions with the enzyme once bound

68

Irreversible inhibition

covalently modifies enzyme, inhibition therefore cannot be reversed. they work by modifying the active site of the enzyme, but do not destroy the overall protein structure

69

how does pH alter enzyme activity?

hydrogen disrupts ionic bonds that contribute to enzyme's shape

70

Allosteric enzymes

an enzyme whose whose activity is modulated through noncovalent binding of a specific metabolite (called an allosteric effector molecule)

they do not follow michaelis menten kinetics

produce a sigmoid curve rather than a hyperbolic curve

71

An allosteric inhibitor pushes the sigmoid to the

right

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An allosteric activator pushes the sigmoid to the

left

73

Acetyl CoA

pyruvate --> oxaloacetate
positive allosteric stimulus is acetyl-CoA


positive allosteric stimulator that stimulates gluconeogensis

rxn
pyruvate --> oxaloacetate

Acts on
pyruvate carboxylase

74

Fructose 2,6 BP

positive effector that stimulates glycolysis

acts on
phosphofructokinase-1

rxn
fructose

75

Citrate

allosteric inhibitor of the Fructose--6P --> fructose 1,6-BP

76

Glucose 6-P

Glucose---> glucose 6--P

negative allosteric effect on hexokinase

77

ATP

positive stimulus on Aspartate carbomylase

rxn

Carbomyl-P + aspartate --> carbamoyl aspartate

in pyrimidine synthesis

78

CTP

allosteric inhibitor of Aspartate carbomylase

rxn

Carbomyl-P + aspartate --> carbamoyl aspartate

in pyrimidine synthesis

79

isozymes

enzymes that resemble one another, have the same substrate to react with. isoforms appear in different tissues

80

MI enzymes that can be measure

LDH-1 2-3 days after MI
CK-MB 12-14 hrs after MI
Troponin I 12-24 hrs after MI
AST/SGOT1 12-16 hrs after MI