Week 3 Flashcards
(167 cards)
1
Q
What are the main general functions of enzymes?
A
They act as biological catalysts.
Stabilise transition states of molecules.
2
Q
How are enzymes ‘catalysts’ ?
A
They lower the activation energy of a chemical reaction by offering an alternative reaction pathway with a lower energy requirement. They also never alter the equilibrium of a reaction.
3
Q
How do catalysts affect the equilibrium of a reaction?
A
They don’t affect it
4
Q
How many times faster do enzymes catalysts make chemical reactions in comparison to reactions that don’t use a catalyst.
A
10^3 to 10^20
5
Q
Do enzyme catalysts work on forward or backward reactions?
A
Both
6
Q
What is meant by enzyme catalysts being stereospecific?
A
They only act on one stereoisomer of a substrate.
7
Q
What is a stereoisomer?
A
Molecules which have the same chemical composition but their atoms are arranged differently in space.
8
Q
How many classes of enzymes are there?
A
6
9
Q
What are the 6 classes of enzymes?
A
Oxidoreductases Transferases Hydrolases Lysases Isomerases Ligases
10
Q
How do oxidoreductases work?
A
They catalyse oxidation and reduction reactions.
11
Q
What do oxidoreductase enzymes often use as a coenzyme?
A
NAD+
12
Q
How do transferase enzymes work?
A
They catalyse group transfer reactions by causing a portion of the substrate molecule to bind covalently to the enzyme. They require the presence of a coenzyme.
13
Q
Give an example of a transferase enzyme.
A
Kinases
14
Q
What is the purpose of hydrolase enzymes?
A
Catalyse hydrolysis reactions
15
Q
What is the purpose of lysine enzymes?
A
Catalyse lysis of substrates
16
Q
Give an example of a use of a Lysase enzyme.
A
The lysine enzyme ‘Pyruvate Decarboxylase’ is used to covert Pyruvate into Acetaldehyde.
17
Q
What cycle are Lysase enzymes used in?
A
Citric acid cycle
18
Q
What do Isomerase enzymes do?
A
They catalyse structural changes in a single molecule.
19
Q
How many reactants and products do reactions using Isomerase enzymes have?
A
1 reactant and 1 product.
20
Q
Give an example of a reaction using an Isomerase enzyme.
A
The conversion of L-alanine to D-alanine.
21
Q
What is another name for ligases enzymes?
A
Synthetases
22
Q
What are the purpose of ligase enzymes?
A
They catalyse ligation but require ATP
23
Q
What molecules do Ligase enzymes require to work?
A
ATP
24
Q
What is ligation?
A
The joining of molecules
25
Give an example of when a Ligase enzyme is used.
L-Glutamate is converted to L-Glutamine by using Glutamine Synthesise enzyme.
26
What are the units of the velocity of a reaction?
s^-1
27
What are the two reactions for calculation velocity of a reaction?
Change in [P] / change in time.
Or
V=k[s]
28
What graph must you plot to work out the initial rate of a chemical reaction?
Concentration of product (Y) against time (X).
Must use more than one concentration of substrate
Initial velocity is the gradient of the initial slope.
29
How do you calculate the rate constant of a reverse reaction?
Change in initial velocity/ change in concentration of substrate.
30
What is the equation calculating the velocity of a reverse reaction with 2 substrates.
V=k[S1][S2]
31
What are the units for for rate constant (k) in a reaction with 2 substrates.
M^-1S^-1
32
What is the rate of reaction of reaction with 2 substrates determined by?
The rate limiting substrate
33
What type of bonding occurs in enzyme substrate complexes.
Non-covalent bonds within the active sites.
| These are transient bonds.
34
What is a first order reaction?
A reaction whose rate is directly proportional to the conversion of only one reactant.
35
What graph must be plotted to calculate Km
Initial velocity against substrate concentration.
36
What is a hyperbolic curve?
A curve which cuts an axis and has symmetry.
37
What is the equation for calculating Km?
Maximum velocity/ 2
38
What does a low Km value indicate?
The lower the Km, the more tightly the substrate is bound to the enzyme.
39
What does Km value of an enzyme indicate?
The stability of an enzyme - substrate complex.
40
What are enzyme inhibitors?
Compounds that bind to an enzyme and interfere with its activity.
41
When are reversible natural enzyme inhibitors frequently used?
In metabolism
42
Describe the binding of reversible artificial enzyme inhibitors to enzymes
Weak non-covalent bonding
43
How do competitive inhibitors affect the Km and maximum velocity of a reaction?
Raise Km
| Dont change maximum velocity
44
How do non-competitive inhibitors affect the maximum velocity and Km of reactions?
Lowers the maximum velocity
| Km unchanged
45
What type of bonding do irreversible enzyme inhibitors have with the enzyme?
Stable covalent bonds
46
When does irreversible inhibition of enzymes often occur?
When there has been alkylation or acylation of the side chains of an amino acid in the active site of an enzyme.
47
How do catalysts affect transition states of molecules?
They stabilise transition states
48
Describe the active site of polar amino acid residues
They have an active site lined with hydrophobic residues and a few polar ionisable residues.
49
What is the purpose of polar amino acid residues in chemical reactions?
They act as co-enzymes
50
What is the purpose of acid-base catalysis of reactions and how does this occur?
Increases the rate of reaction by transferring protons.
51
What does acid-base catalysis often rely on?
Amino acid side chains that can donate and accept protons at physiological pH.
52
During covalent catalysis, what do the reactive side chains act as?
Nucleophiles or electrophiles
53
What is a nucleophile ?
a species which is strongly attracted to a region of positive charge in another molecule.
They have a full negative or slight negative charge.
54
What is an electrophile?
A spaces which is attracted to an electron-rich, negative region in another molecule.
They have a full positive or slight positive charge somewhere.
55
What are the 2 types of co-factors?
Essential ions and coenzymes
56
What are the types of essential ion cofactors?
| Describe the binding of each
Activator ions - loosely bind
| Prosthetic groups - tightly bind
57
What are the type of coenzyme cofactors? Describe the binding of each
Co-substrates - loosely bind
| Prosthetic groups - tightly bind
58
What is an acid catalyst?
Amino acid side chains of enzymes which are capable of donating protons (H+).
59
What is a base catalyst?
Amino acid side chains on enzymes which donate electron pairs to stabilise protons in the form of H+.
They can also accept protons (H+).
60
What is the induced fit model of catalysis?
The substrate does not have to fit the active site of the enzyme perfectly. As the substrate binds to the active site, the active site changes shape slightly and they become complimentary. An ES complex can therefore be formed.
61
What are the 2 main steps in covalent catalysis?
1. Covalent bonds form between the enzyme and substrate to form reactive intermediates.
2. The covalent bonds are broken to regenerate the original enzyme formation.
62
What is the purpose of nucleophiles in covalent catalysis?
They are used to stabilise carbonyl groups by attacking electrophiles.
63
How many energy peaks does a covalent catalysis reaction have and why?
2 because it is a 2 part reaction.
64
How can a reaction which is covalently catalysed be identified by its energy graph?
It will have 2 peaks.
65
What does the valley between the 2 peaks of an energy graph for a covalently catalysed reaction show?
It shows the energy of the intermediate formed by the substrate making covalent bonds with the enzyme to form an ES complex.
66
What is the intermediate complex of a covalently catalysed reaction.
The enzyme-substrate complex.
67
What type of reactions occur during metal ion catalysis?
Oxidation and Reduction (Redox)
68
What does the metal ion do to act as a catalyst in reactions?
It may interact directly with the substrate or it may be used to stabilise the transition state of the substrate.
69
Are intramolecular reactions or intermolecular reactions generally faster?
Intramolecular reactions
70
What is entropy?
The measure of disorder of a reaction and therefore a measure of the energy that is unavailable to do work.
71
How does the entropy alter in a forward intermolecular reaction change and why?
In intermolecular reactions, one molecule is made for every 2 that react and so the entropy tends to decrease.
72
How do enzymes catalysing intermolecular reactions use the proximity effect and what effect does this have?
Enzymes bind the substrates close together in the active site of the enzyme. This means that the reactive groups of the substrate are appropriately orientated for the reaction. This means the reaction will occur alot faster.
73
How do enzymes affect the equilibrium of a reaction.
Cause no change
74
What parameters effect the efficiency of an enzyme when catalysing a reaction ?
Substrate concentration, enzyme concentration, temperature, pH.
75
Why do graphs showing rate of enzyme catalysed reactions eventually plateau?
Either substrate or enzyme concentration becomes a limiting factor.
76
What are the unite for rate of a first order reaction?
S^-1
77
What is Beer Lambert law used for ?
To relate a UV spectroscopy absorbency reading to concentration of a specific substance.
78
What is beer lamberts equation and what does each letter mean?
A = E x c x l
```
A = UV absorbency reading
C = product concentration
L = path length
```
79
What is the path length of a cuvette ?
1cm
80
What is absorbency directly proportional to in an enzyme catalysed reaction?
Product concentration
81
What is velocity directly proportional to in an enzyme catalysed reaction?
Substrate concentration
82
What are the units of concentration ? Write correctly.
moles/L
| Miles per litre or dm^3
83
Define moles.
The mass of a substance compared with 1/12th the mass of Carbon 12.
84
What is the difference between moles and molarity?
Molarity takes into account the concentration of a substance in a specific volume.
Moles have show a relative mass
85
What are Machakis Menton kinetics used for?
Calculating the rate of enzyme catalysed reactions.
86
How is initial rate calculate on a Machalis Menton graph?
Using the gradient of a line which is linear from (0,0) and is suited to the plotted line.
87
What must be the initial rate of reaction for all Machalis Menton graphs?
(0,0)
88
How can gradient of a graph be calculated.
(Change in y value) / ( change in x value)
89
What equation is used to identify the equation of a straight line on a graph?
Y=Mx + c
90
How is vMax plotted on a graph?
Dashed straight line
91
Why is the VMax always plotted above the data you have recorded on a Mechalis Menton graph ?
You must always assume the values will increase
92
What is Km a measure of ?
The stability of an enzyme-substrate complex
93
Why can vMax be described as a hyperbolic graph plot?
It is plotted beyond the values which have already been obtained so is an exaggeration of the exact data.
94
What does a low Km value of an enzyme suggest?
Tight binding between the enzyme and the substrate.
95
What does a high Km value indicate ?
Loose binding between an enzyme and a substrate
96
What effect does a catalyst have on a chemically unfavourable reaction ?
It won’t have an effect
97
How does Ea affect rate of reaction?
The greater the activation energy, the slower the rate of reaction.
98
What characteristics does an energetically favourable reaction have?
Less stable reactants than products.
99
Why are only small amount of catalysts needed in a reaction ?
They are never chemically changed or used up
100
Give examples of some non-specific enzymes.
Metals such as ;
Platinum
Zinc
101
What is another name for an enzymes active site
Cleft
102
What determines the specificity of an enzyme?
The shape of its active site.
| Charges within the active site.
103
How many amino acids are involved in the specific binding between an enzyme and a substrate ?
3-10
104
What type of bonds form between an active site and a substrate molecule?
Ionic interactions
Hydrogen bonds
Hydrophobic interactions
105
What are the issues that can arise from specific enzyme substrate bonding forming?
If a mutation of just one amino acid occurs in the active site, this can lead to complete loss of specificity of an enzyme.
106
What must be true for an enzyme substrate complex to correctly form?
The substrate must adopt the correct orientation to favour the reaction being catalysed.
107
What happens to complete the formation of an ES complex once the enzyme is bound to the substrate?
Slight movements of the protein backbone in the enzyme induce strain in bonds between atoms of the substrate. This moves the substrate molecule into a transition state.
108
Why is a transition state substrate better for forming an ES complex than an initial state substrate?
Transition state substrates bind more strongly to the active site.
109
What is the purpose of the conformational change of the substrate once bound to the active site of an enzyme?
It enables the substrate to enter its transition state which is more stable and can form more molecular forces with the active site of the enzyme.
110
Why is the product of a reaction immediately released from an enzyme during most chemical reactions?
The product of the reaction will not bind specifically to the enzyme as they do not have complimentary shapes and therefore cannot form a close association with many molecular bonds.
111
Which part of enzymes can partake in chemical reactions?
The amino acid residue side chains of the enzyme can undergo chemical reactions.
112
What effects do allosteric binding have on an enzyme?
Allosteric binding can cause conformational changes in an enzyme meaning that its function is altered.
This can help increase or may often decrease the rate of enzyme catalysis of a reaction.
113
What are the limitation of enzymes ?
Sensitive to pH and temperature.
114
Outline the effects of increase temperature on rate of reaction.
Initially increases before the temperature becomes too high and causes denaturation or enzymes. At this point rate decreases and eventually falls to zero.
115
Why do enzymes loose their catalytic ability if pH becomes too high?
This intramolecular forces are disrupted and their active sites are caused to change shape. This means the active site is no longer complimentary to the required specific substrate.
116
What type of organisms are able to survive at temperatures above 60 degrees?
Hyperthermophiles
117
How are thermophiles able to survive at extremely high temperatures?
They maintain a 3D structure even in high temperatures due to having extensive intramolecular bonds and lower amounts of Glycine amino acid (which normally causes protein flexibility).
They have heat stable DNA
118
What characteristic does the presence of Glycine give in amino acid chains?
Flexibility
119
What enzymes do thermophiles employ to ensure they have tightly packed DNA?
DNA Gyrase
120
What are the purpose of DNA binding proteins in enzymes?
They help maintain the correct folded structure
121
How does pH denature enzymes?
If the pH is outside the narrow optimum range, the non-covalent interactions that hold the enzyme into its functional folded shape, will be disrupted. This will cause the enzyme to become non-functioning.
122
How does initial reaction rate vary with substrate concentration varying?
Higher initial substrate concentration results in a higher initial rate of reaction
123
What is VMax of a reaction?
The maximum rate of velocity of an enzyme-catalysed reaction.
124
Which is there a plateau in reaction rate once the VMax is being approached?
At VMax, the enzyme is working at full capacity and every active site has a substrate bound to it. Enzymes are saturated
125
What is enzyme saturation?
Every active site is bound to a substrate. The enzymes are working at their maximum rate.
126
What is the turnover number of an enzyme ?
The number of substrate molecule processes by an enzyme molecules per second.
127
What does Kcat stand for?
Turnover number of an enzyme
128
Define Michaelis constant.
The concentration of substrate that is required for an enzyme to operate at one half its maximum velocity.
129
What is the abbreviation for michaelis constant ?
Km
130
What does Km value of a reaction indicate about substrate concentration ?
When Km is large, there is more substrate present because it can only loosely bind to the enzyme.
When Km is high, there is less substrate present because it is more tightly bound to the enzyme.
131
What value can indicate the concentration of substrate at 1/2 VMax of a reaction?
The Km
132
What type of Km enzymes will a substrate be more likely to bind to and why?
Substrate is more likely to bind with an enzyme of low Km because it will make a more stable association with this enzyme type than one of high Km.
133
What causes substrates with a low Km to be converted readily to product even at low concentration?
The reaction will be catalysed efficiently due to strong association between the enzyme and substrate
134
Does a rate curve ever reach VMax?
No. VMax is an asymptote.
135
What is the asymptote of a rate equation?
The VMax line
136
What would have to be true for VMax of a reaction to be reached theoretically?
An infinitely high substrate concentration would be required
137
Equate the Lineweaver-Buck equation to y=Mx+c.
```
Y= 1/v
M= (KM)/(VMax)
X= 1/[s]
C= 1/ VMax
```
138
What is the overall purpose of enzyme inhibitors?
To reduce enzyme activity
139
Are enzyme inhibitors naturally occurring or synthetic?
Can be both
140
Where in enzymes do inhibitors act?
On the active site or allosteric sites.
141
What type of molecules are most enzyme inhibitors?
Small organic molecules or ions.
142
What are the 2 main categories of enzyme inhibitors?
Reversible
| Irreversible
143
Give an example of an irreversible enzyme inhibitor.
Aspirin
144
Describe the binding of irreversible enzyme inhibitors to enzymes.
Tightly bound by covalent bonds between the amino acid residues within the active site of the enzyme.
145
Describe the usual shape of irreversible enzyme inhibitors.
Usually similar to the substrate of that enzyme so are complimentary.
146
Describe the binding of reversible enzyme inhibitors to enzymes.
Bind non-covalently by hydrogen bonding, ionic interactions, can der walls forces or via hydrophobic interactions.
147
What are the 3 types of reversible enzyme inhibition?
Competitive
Uncompetitive
Non-competitive
148
What is competitive reversible enzyme inhibition?
An inhibitor which has a similar structure to the desired substrate binds to the active site of an enzyme to form an enzyme inhibitor (EI) complex.
149
Describe uncompetitive reversible enzyme inhibiton
An inhibitor binds to an allosteric site after the substrate has bound to form a enzyme substrate inhibitor complex (ESI).
150
How can uncompetitive enzyme inhibiton be reversed?
By increasing substrate concentration
151
What complex type is formed by noncompetitive enzyme inhibition?
Enzyme substrate inhibitor complex
152
What type of enzyme inhibiton is reversed by increasing substrate concentration?
Uncompetitive
153
How do the formation of EI and ESI complex reduce reaction rate ?
They can’t form products and reduce the number of active sites available to create ES complex. Product formation is reduced.
154
How do uncompetitive enzyme inhibitors affect Km and VMax.
No effect
155
What effect does competitive inhibition have on VMax of a reaction and why?
Under high substrate concentration conditions.
No change to VMax because substrate binding to the active site isn’t impeded.
Inhibitors is competed out of the active its by substrate
156
How does Km alter when inhibitor concentration alters in competitive enzyme inhibiton?
As the amount of inhibitor increases, the amount of free enzyme angle to react with the substrate decreases. So Km increases
157
What is the melting temperature of a protein specific to?
The specific order and quantity of amino acids.
158
What is the purpose of an enzyme inhibition constant in Mechalis menton kinetics?
To define the equilibrium of reaction which is being enzymatically inhibited.
159
Outline the equation showing the catalysis 4-nitrophenyl phosphate by Acid phosphatase.
Acid Phosphatase + 4-nitrophenyl phosphate
=
4-nitrophenyl + Pi
160
How does a U.V spectrometer measure the absorbency of a given sample?
They create a ratio of the light intensity supplied with the light intensity which penetrates the molecules.
161
What is the UV spectrometry absorbance reading of a sample a ratio of ?
The light intensity supplied to the sample compared with the light intensity that penetrates the sample.
162
What is the formula for Beer Lamberts law?
A = E x c x l
163
What is extinction coefficient specific to?
Different DNA, RNA and protein molecules.
164
What wavelength is used to measure absorbency of a protein on a U.V. spectrophotometer?
280nm
165
What wavelength is used to measure absorbency of RNA or DNA on a U.V. spectrophotometer?
260nm
166
What does gradient of a Beer Lamberts graph show?
Extinction coefficient
167
What are the units of Beer Lamberts extinction coefficient?
M^-1 cm^-1
