Enzymatic Catalysis Flashcards
(104 cards)
1
Q
The unique physical and chemical properties of the active site limit what?
A
an enzyme’s activity to specific substrates and reactions.
2
Q
What may require metal ions or organic co factors?
A
some enzymes
3
Q
What occurs when enzymatic reactions take the slowest steps?
A
Will exert the most control.
4
Q
What is an enzyme?
A
a protein
5
Q
RNA models can function as what?
A
catalyst
6
Q
Most chemical reactions are driven by what?
A
catalyzed by an enzyme.
7
Q
What makes reaction rates go faster?
A
enzymes
8
Q
Why are enzymes useful to living things under mild reaction conditions?
A
Reactions will occur under conditions not optimal for reaction rates….. different temperatures.
9
Q
With an enzyme, what type of side reactions are avoided?
A
ones that may have deleterious effects are usually avoided.
10
Q
Enzymes have what type of specificity?
A
greater reaction specificity
11
Q
What has the capacity of regulation?
A
an enzyme; we may not want this reaction to occur all the time.
12
Q
What is the main thing that an enzyme is known for?
A
make a chemical reaction proceed faster than normal.
13
Q
How much faster can en enzyme make a reaction go?
A
million folds faster.
14
Q
What does oxidoreductases catalyze?
A
Oxidation-reduction reactions
15
Q
What type of reaction does transferases catalyze?
A
Transfer of function groups.
16
Q
Oxidoreductases takes off what to form energy?
A
Hydrogen
17
Q
What enzymes breaks bonds by water addition?
A
hydrolases
18
Q
What type of chemical reaction is catalyzed by hydrolases?
A
hydrolysis reactions.
19
Q
What type of chemical reaction is catalyzed by the enzyme lyases?
A
group elimination to form double bonds.
20
Q
What type of enzyme is needed to catalyze an isomerization?
A
Isomerases
21
Q
What does the enzyme isomerase do in the catalysis of the reaction?
A
rearrange molecules.
22
Q
What type of enzyme is used for the bond formation coupled with ATP hydrolysis?
A
ligases
23
Q
In the bond formation coupled with ATP hydrolysis, Ligase does what?
A
tries to conserve energy.
24
Q
In enzymes, the exact fir may not be as obvious from their independent structures, why?
A
binding may require an adjustment on the part of the enzyme.
25
What is it called when an adjustment on the part of the enzyme is done?
induced fit.
26
Enzymes encounter substrates as 3 dimensional objects much like what?
antibody
27
In stereospecifc enzymes-substrate interaction may require what?
stereospecificity on the part of the enzyme.
28
What does Chymotrypsin do?
cleaves polypeptide bonds.
29
Is chymotrypsin specific?
no, not completely specific for a peptide bond but can catalyze the same hydrolysis with esters.
30
What enzyme can catalyze same hydrolysis with esters?
Chymotrypsin.
31
What do many enzymes require?
auxiliary molecules, or cofactors to help them with chemistry.
32
Cofactors expand the range of enzymatic reactions. What can cofactors be broken down to?
metal ions and coenzymes.
33
Where are co-enzymes typically derived from?
Vitamins
34
What can coenzymes can be subdivided into?
cosubstrates and prosthetic groups.
35
What are cosubstrates?
they are dissociable
36
What are prosthetic groups?
They are permanently bound once bound.
37
Hemoglobin is an example of what group and why?
a prosthetic group because the heme molecule is stuck on the protein and can't dissociate once it is bound.
38
What does an enzyme provide in terms of a reaction other than speed?
a lower-energy pathway from substrate to product.
39
What does not affect the overall free energy change for reactions?
Enzyme
40
Describe the relationship between equilibrium reaction and an enzyme?
it will not disrupt the equilibrium of any reaction.
41
The higher the transition rate what occurs?
The slower the reaction will occur.
42
The higher the change of G (Gibbs Free Energy) What occurs?
The slower the reaction.
43
When a step is slow what can be determined?
It is rate limiting
44
What can lower free energy?
Enzymes will lower the free energy of the transition state.
45
If a reaction goes faster due to an enzyme what will it not effect?
the change of G of the overall reaction nor its equilibrium.
46
What are curved arrows used for in drawing chemical reaction mechanisms?
shows movement of electrons vs old and new chemical bonds.
47
What can be commonly said about the transition state?
Something you will never see in life.
48
What can be seen when a general acid is catalyzed?
A proton is donated.
49
What be said was catalyzed when a proton is extracted?
base was catalyzed.
50
Acid-Base catalysis involves what?
a proton transfer
51
What occurs when a proton is donated by an acid?
Acid is catalyzed.
52
What occurs when a proton is extracted by a base?
Base is catalyzed.
53
What does the structure of the bovine pancreatic RNAse S do?
hydrolyzes RNA.....adds water across a phosphodiester bond.
54
In the RNAse A reaction His- 12 acts as what?
a general base.
55
In an RNase A mechanism what does His-119 act as?
a general acid
56
Why is it important that His-12 acts as a general base and His-119 act as a general acid?
to promote nucleophilic attack and bond cleavage.
57
In the RNase A mechanism His-12 acts as a general acid in step 2 and His-119 acts as a general base, why?
to promote hydrolysis.
58
What is an important feature of the bovine pancreatic RNase S enzyme?
the original enzyme is restored intact and unmodified.
59
Does an enzyme turn off when it is over?
no an enzyme doesn't, if it does then it is not an enzyme. It can do more than one reaction. It doesn't just simply do one reaction.
60
What does covalent catalysis usually involve?
a nucleophile
61
The catalyst is the nucleophile and does what to the substrate?
attack the substrate to form a covalent bond.
62
When covalent catalysis occurs what happens to electrons?
the electrons of the reaction center withdraw.
63
What is step 3 of covalent catalysis?
the catalyst leaves in a reversal of step 1
64
Why must step 3 need to be as efficient as step1?
the amino acid of the enzyme needs to be a good leaving group.
65
What are examples of unprotonated groups?
Lys, His, Cys, Asp, and Ser
66
What do biologically important nucleophilic groups do?
donate an electron pair to an electrophile to form a chemical bond.
67
What are the 4 groups that are good nucleophiles?
hydroxyl, sulfhydryl, amino, and imidazole.
68
When metal ions act as enzyme cofactors, what orients a proper reaction?
binding substrates
69
What mediates oxidation-reduction reactions?
Metal ions oxidation states
70
Metal ions are responsible mainly for what?
electronic stabilizing or shielding negative charges.
71
What are biologically important electrophilic groups?
protons, metal ions, carbonyl carbon atom, and cationic imine.
72
What is a schiff base?
a cationic imine
73
What is the definition of an electrophile?
positively charged or neutral groups attracted to electron.
74
What is the role of Zn 2+ in carbonic anhydrase?
3 His residues will chelate the zinc.
75
Zn 2+ in carbonic anhydrase will use CO2 why?
as a catalyze in blood stream.
76
What is a transition state?
an intermediate in a chemical reaction that shares structure with both the substrate and the product.
77
An enzyme can have higher affinity for what?
the transition state than for either the substrate or the product of the reaction.
78
The greater the affinity for the transition state what occurs to the reaction?
the faster the reaction will be catalyzed.
79
What is an example of inhibition by transition state analogs?
enzyme proline isomerase and it can interconvert proline into a D isomer from an L isomer.
80
These analogs are potent inhibitors that demonstrate what?
their affinity for the enzyme
81
What will lysozyme cleave?
bacterial cell wall and the polysaccharide part of the cell wall.
82
In a lysozyme-substrate interaction what occurs to the 6 sugar residues around the substrate cleavage?
site are contacted by hydrogen bonds with amino acid R groups of the enzyme.
83
In the lysozyme-substrate interactions how many amino acids are directly involved in catalysis?
2
84
What is step 1 in the lysozyme reaction mechanism?
Polysaccharide substrate binds enzyme and distorts the D residue
85
Why in the lysozyme reaction mechanism does Glu-35 protonated at neutral pH?
The environment is very hydrophobic and this shifts its pKa
86
What occurs once step 1 in the lysozyme reaction mechanism reaction to Glu-35?
Donates its proton to initiate cleavage site.
87
What occurs in lysozyme reaction mechanism in step two?
general acid catalysis. Asp 52 nucleophyllically attacks the electron poor C1 to form a substrate-enzyme covalent intermediate.
88
What occurs in the lysozyme reaction mechanism in step 3?
covalent catalysis and then onward to the covalent intermediate.
89
What is step 4 of the lysozyme reaction mechanism?
water binding, water replaces the E residue in the active site.
90
What occurs in step 5 of the lysozyme reaction mechanism?
General base catalysis occurs and Glu 35 assists with the addition.
91
What is there to note on the lyzsozyme: transition state analog inhibitor?
the rings are planar supporting the half chair conformation of reisdue D
92
What were identified by chemical labeling and structural analysis?
catalytically active Ser, His, and Asp residues of Serine proteases.
93
What does a binding pocket determine?
the substrate specificity of the various proteases.
94
What does the Serine Protease catalyze?
peptide bond hydrolysis
95
How does the Serine proteases catalyze the peptide bond hydrolysis? (5 ways)
proximity and orientation effects, acid base catalysis,covalent catalysis, electrostatic catalysis, and transition state stabilization.
96
What are Zymogens?
inactive precursors of enzymes
97
What is the specificity of chymotrypsin?
Cleavage specificity on the carboxyl side of large aromatic R groups.
98
What is chymotrypsin?
a protease
99
What does chymotrypsin do?
breaks peptide bonds.
100
Chymotrypsin is the reverse of what?
the synthesis of bond and all have amino acid side chains specificity.
101
Describe chymotrypsin?
Red is active site and next to that little cleft that is coated with hydrophobic residues.
102
What type of adduct does chymotrypsin have?
Covalent peptide adduct.
103
What do enzymes form?
covalent intermediates with their substrates.
104
How do enzymes differ from ordinary chemical catalyst?
in reaction rate, reaction conditions, reaction specificity, and control.
