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Flashcards in rice Deck (67):
1

where do the names of enzymes come from

its substrate or the chemical reaction it catalyses

2

what is the transition state

a transient entity formed in the conversion of reactants into products

3

what is the maximum energy point along a reaction path

the transition state

4

is the transition state an intermediate

no

5

the larger the net free energy of a reaction the more...

irreversible a reaction

6

what is the relationship of the free energy of reactants and products in an exothermic reaction

products of lower free energy than reactants

7

what is different about a 2 step reaction compared to a 1 step one

an intermediate is formed in the conversion of reactants to products

8

what did linus pauling think enzyme catalysis resulted in

lowering of the transition state

9

what sorts of catalysis do enzymes use (6)

covalent catalysis (nucleophilic/electrophilic)
acid catalysis
base catalysis
metal ion catalysis
conformational organisational catalysis

10

what type of enzyme is cystein a key amino acid in functional group

thiol proteases

11

what is the intermediate when an enzyme with a cysteine containing functional group is used

acylthiolenzyme

12

what enzyme contain a serine/threonine functional group

serine proteases
glutamine synthetase

13

what is the intermediate produced by serine proteases

acylenzyme

14

what enzyme contains an aspartate functional group

lysozyme

15

what enzyme contains a lysine functional group

DNA ligase

16

serine and threonine have a pKa f 15, why

alcohol anion has no resonance structure

17

tyrosine has a pKa of 10 (acidic) why?

phenolate anion has 4 resonance structures

18

aspartic acid and glutamic acid have a pKa of 4.5, why?

carboxylate anion has 2 resonance structures

19

lysine has a pKa of 10 thus a weak and strong base, why?

the primary amino group has no resonance structures

20

what are serine proteases an example of

nucleophilic covalent catalysis

21

what is an example of a serine protease

chymotrypsin

22

what does chymotrypsin use as a nucleophilic covalent catalyst to form as acyl-enzyme intermediate

CH2-OH group of Ser-195

23

what is used as a proton donor/acceptor in the reaction catalysed by chymotrypsin

His-57

24

what bond do proteases cleave

scissile bond

25

proteases gave one or more ....... ...... ...... which can select for certain types of side chain

substrate specificity pockets

26

which substrate specificity pockets are upstream of the scissile bond

S1, S2 and S3

27

which substrate specificity pockets are downstream of the scissile bond

S1', S2', S3'

28

where is the main specificity site after which cleavage occurs in proteases

pocket S1 which binds residue p1-p1

29

is the specificity group after which cleavage occur the same or different for different enzymes

different

30

what properties does the specificity group after which cleavage occurs of trypsin have

basic

31

what properties does the specificity group after which cleavage occurs of chymotrypsin have

aromatic or big hydrophobic

32

what are the key residues of chymotrypsin

Ser 195
His 57

33

what molecule modifies the crucial Ser 195, totally inhibiting the enzyme

PMSF

34

what molecule blocks serine proteases and other related molecules

DIPF

35

how does TPCK inhibit the enzyme

binds enxyme active site and induces nucleophilic attack by His
enzyme is not inactive as His57 is modified

36

where the essential residues of His 57 and Ser 195 found

deep in the cleft with Asp 102

37

what 3 residues form the catalytic triad

His 57
Ser 195
Asp 102

38

what does interaction of the catalytic triad make it easier to do

stabilise a negative charge on Ser 195

39

what does the negative charge on the Asp 102 stabilise

the formation of the +ve form of His 57 - helping His 57 grab Ser 195s proton

40

when Ser 195 loses its proton what does it become

nucleophilic - highly reactive against substrates or inhibitors with a + charge

41

without Asp 102 what is the rate of catalysis of chymotrypsin compared to the wild type

0.05%

42

other than the catalytic triad, what is another important feature of chymotrypsin

oxyanion hole

43

what is the oxyanion hole

region in the active site where the backbone amide hydrogens of Serine 195 and glycine 193 point into the active site cavity

44

what intermediate is established by chymotrypsin

tetrahedral enzyme substrate intermediate

45

the oxyanion hole increase the activity of the enzyme by a factor of what?

10,000

46

what is the mechanism for chymotrypsin

Ser195 attacks the unreactive carbonyl group of the substrate
enzyme briefly becomes covalently bonded to the substrate formin a tetrahedral intermediate whose -ve charge is stabilised by the oxyanion hole
1. tetrahedral intermediate decomposed to acyl enzyme intermediate (His57 acting as an acid)
2. enzyme is deacylated through another tetrahedral intermediate. (water is the attacking nucleophile and Ser195 is the leaving group
3. this returns the enzyme to its original state

47

what do trypsin, chymotrypsin and elastase share

a common fold

48

how does recognition of the substrate backbone occur

antiparallel b-sheet formed between substrate and protein

49

what do enzymes such as chymotrypsin need to activate them

proteolytic cleavage of their precursors

50

what is the precursor of chymotrypsin

chymotrypsinogen

51

what is the key step of the blood clotting activation cascade

the serine protease thrombin cleaves an arg-gly bond in the soluble fibrinogen - plaques of insoluble fibrin which form clots and scabs to prevent bleeding

52

what is special about subtilisin and chymotrypsin

completely unrelated sequences and structures but have evolved to converge on the same solution to carrying out a proteolysis reaction - a catalytic triad

53

what is an example of an aspartyl protease and what does it do

HIV protease. dimeric enzyme that is a target for drug discovery die to its role in virus maturation

54

in the active site of the HIV protease 2 aspartates clamp what kind of molecule which acts as the attacking nucleophile

water

55

what kind of protease do many fruits contain

cysteine protease

56

what is an example of a cysteine protease

papain

57

what does papain use to form an ion pair

SH group of Cys 25 and the imidazole of His 159 to form an ion pair

58

what type of anion does the papain enzyme have that attacks the peptide bond

nucleophilic thiolate

59

in the second part of the papain reaction what is used as a nucleophile to hydrolyse the thiol ester and form the carboxylate as a second product

water

60

what do threonine proteases use as a nucleophile

hydroxyl of Thr

61

what do cysteine proteases have

a His-cys diad

62

what do all proteases have in common (3)

- a nucleophile is activated by another part of the active site
- other groups on the enzyme polarize the carbonyl group of the peptide that is to be cleaved
- a negatively charged tetrahedral intermediate is produced which is stabilised by the enzyme
-intermediate then collapses to produce a cleaved peptide

63

what do members of the enolase superfamily use to facilitate catalysis

enzyme bound magnesium ion

64

what is the representative member of the enolase superfamily

mandelate racemase

65

what does the reaction of mandelate racemase proceed through? which intermediate?

aci-carboxylate intermediate which is stabilised bu the metal ion

66

what is tetrahydrolipstatin

a potent phospholipase inhibitor used to treat obesity

67

how do lipstatin inhibitors of pancreatic lipase work

- the active site of the enzyme is covered by a lid like domain but is opened by interaction with colipase to make the site available to the substrate
-lipstatin inhibitor interacts with the serine at the active site inhibiting the enzyme