Chapter 4 - Enzymes Flashcards
(142 cards)
1
Q
Define enzymes - short
A
Biological catalysts
2
Q
Break down the phrase biological catalyst
A
Biological’ = they function in living systems
‘Catalysts’ = speed up the rate of chemical reactions without being used up or undergoing permanent change
3
Q
Define catalyst
A
speed up the rate of chemical reactions without being used up or undergoing permanent change
4
Q
Anabolic
A
Build up
5
Q
Catabolic
A
Break down
6
Q
What do globular proteins have
A
Complex tertiary structures
7
Q
What is controlled by enzymes
A
Metabolic pathways
8
Q
How are enzymes produced
A
via protein synthesis inside cells
9
Q
Types of catalysts - 2
A
intracellular or extracellular
10
Q
What are intracellular enzymes
A
produced and function inside the cell
11
Q
What are extracellular enzymes
A
secreted by cells and catalyse reactions outside cells
12
Q
Examples of extracellular protein
A
digestive enzymes in the gut
13
Q
Names example of intracellular protein
A
Catalase
14
Q
Function of catalase
A
- Hydrogen peroxide is produced as a byproduct of many metabolic reaction = harmful to cells.
• Catalase converts hydrogen peroxide into water and oxygen, preventing any damage to cells or tissues.
15
Q
Named example of extracellular enzymes
A
Amylase and trypsin
16
Q
Function of amylase
A
- Involved in the carb digestion
- hydrolyses starch into simple sugars
17
Q
is digestions usually carried our by intracellular or extracellular proteins
A
Extracellular
18
Q
Why is digestions usually carried our by extracellular proteins
A
Because macromolecules being digested are too large to enter cell
19
Q
Where is amylase secreted from
A
Salivary glands + pancreas
20
Q
If amylase is secreted from the salivary gland where is it digesting starch
A
Mouth
21
Q
If amylase is secreted from the pancreas where is it digesting starch
A
Small Intestine
22
Q
Where is trypsin secreted from
A
Pancreas
23
Q
Where does trypsin go
A
Small intestine
24
Q
Function of trypsin
A
• Breaks down proteins into peptides + amino acids
25
Which organisms only use extracellular digestion
Fungi / hyphae
26
How do some organisms only use extracellular digestion
secrete the necessary enzymes directly onto the food they are consuming (e.g. wood) so that the food is digested into smaller, simple molecules that the fungi can then absorb through the walls of the hyphae
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Where do substrates bind on the enzyme
Active site
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Main feature of the active site
Specific shape
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What does the active site having a specific shape mean
Can only bind to a specific substrate
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How can the active site be denatured
PH / temp
31
How does an enzyme substrate complex form
• substrates collide with enzyme active site
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What must happen to form an enzyme substrate complex
must happen at correct orientation + speed for reaction to occur
33
What is metabolism
sum of all different reactions and reaction pathways happening in a cell or an organism
34
What is enzyme specificity a result of
complementary nature between shapes
35
How is the shape of active sister determined by DNA
• shape of active site = determined by complex tertiary structure
o proteins = formed from chains of amino acids
o order of amino acids = determined by DNA
o change DNA / amino acids = change 3D shape
36
What is an enzyme substrate complex
• forms when an enzyme and substrate join
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Key point about enzyme substrate complex
• only formed temporarily before enzyme catalyses reaction + products released
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What is an enzyme product complex
• Substrate(s) then react, and product(s) are formed = enzyme-product complex formed.
39
Define active site
an area within the tertiary structure of the enzyme that has shape which is complementary to shape of a specific substrate molecule.
40
Describe the lock and key hypothesis
• Like a key, only specific substrate will ‘fit’ the active site of an enzyme = lock and key hypothesis
• When substrate is bound to active site = enzyme-substrate complex formed.
• Substrate(s) then react, and product(s) are formed = enzyme-product complex formed.
• Products then released, enzyme is left unchanged, able to take part in subsequent reactions.
41
How are substrates held in enzymes
In a way that right atom-groups are close enough to react.
42
How do R groups interact with enzyme
• R-groups within active site of enzyme also interact with substrate → temporary bonds
• Put strain on bonds within substrate – helps reaction along
43
Describe the induced fit hypothesis
• Active site of enzyme changes shape slightly as substrate enters.
• Initial interaction between enzyme and substrate – relatively weak, but these weak interactions rapidly induce changes in enzymes tertiary structure that strengthen bonding = putting strain on substrate molecule
• This can weaken a particular bond(s) in substrate, lowering activation energy needed for reaction.
44
What are the changes in induced fit called
Conformational changes
45
Define activation energy
Minimum amount of energy required to start a reaction
46
How do enzymes speed up chemicals reactions
reduce the stability of bonds in the reactants
o The destabilisation of bonds in the substrate makes it more reactive
47
How to enzymes work
providing an alternative energy pathway with a lower activation energy
48
How do enzymes help organisms
• Without enzymes, extremely high temperatures or pressures would be needed to reach the activation energy for many biological reactions
o Enzymes avoid the need for these extreme conditions(that would otherwise kill cells)
49
How does changing the pH denature an enzyme
o Hydrogen and ionic bonds hold the tertiary structure of the protein (ie. the enzyme) together
o Below and above the optimum pH of an enzyme, solutions with an excess of H+ ions (acidic solutions) and OH- ions (alkaline solutions) can cause these bonds to break
o The breaking of bonds alters the shape of the active site, which means enzyme-substrate complexes form less easily
o Eventually, enzyme-substrate compl exes can no longer form at all
o At this point, complete denaturation of the enzyme has occurred
50
What holds the tertiary structure together in enzyme
o Hydrogen and ionic bonds
51
What does the location of an enzyme indicate
It’s optimum environment
52
Where is pepsin found
Stomach
53
What does pepsin being found in the stomach indicate
Suited to an acidic environment at pH 2
54
Why does the stomach have a pH of 2
due to the presence of hydrochloric acid in the stomach’s gastric juice
55
What are buffer solutions
Solution = Have a specific pH
56
Purpose of buffer solutions
maintain pH through reaction
57
When we are investigating the effect of pH on enzymes - what should we test it kn
• Use the enzyme amylase to breakdown starch at a range of pH values,
58
What does amylase do
digests starch (a polysaccharide of glucose) into maltose (a disaccharide of glucose)
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What would we use to test for presence / lack of starch
Iodine
60
Cokour change of iodine in pH practical + what that means to breaking down starch
61
Method - Investigating the effect of pH on enzyme reaction rates for starch
• Place single drops of iodine solution in rows on the tile
• Label a test tube with the pH to be tested
• Use the syringe to place 2cm3 of amylase in the test tube
• Add 1cm3 of buffer solution to the test tube using a syringe
• Use another test tube to add 2cm3 of starch solution to the amylase and buffer solution, start the stopwatch whilst mixing using a pipette
• After 10 seconds, use a pipette to place one drop of the mixture on the first drop of iodine, which should turn blue-black
o This test indicates whether starch is still present
• Wait another 10 seconds and place another drop of the mixture on the second drop of iodine
• Repeat every 10 seconds until iodine solution remains orange-brown
• Repeat experiment at different pH values
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What colour is iodine solution
Organe - brown
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How do we control variables
o Equal volume and concentration of enzyme should be used in each test tube
o Equal volume and concentration of the substrate (starch) should be used
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What does it mean when the solution remains orange brown
amylase has broken down all of the starch so nothing is left to react with the iodine
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How to interpret results from - Investigating the effect of pH on enzyme reaction rates
less time the iodine solution takes to remain orange-brown, the quicker all the starch has been digested and so the better the enzyme works at that pH
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Limitations of starch + iodine = pH = practical
Colour = difficult to distinguish = use a colorimeter
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How can this practical be adapted to control temperature
using a water bath at 35℃
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How does temp effect rate of reaction
• higher temp = increases kinetic energy = increases number of collisions
• higher temp = increases potential energy = increases proportion of successful collisions
• speeds up rate of reaction
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How does increased temp denature enzymes
• increased kinetic energy of = puts a strain on enzymes = causing the weaker hydrogen and ionic bonds to break
• breaking of bonds causes the tertiary structure of the protein (i.e. the enzyme) to change
• The active site is permanently damaged and its shape is no longer complementary
• Denaturation has occurred if the substrate can no longer bind
70
What temp do enzymes denature at in humans
Most denature at temps over 60
71
Optimum temp in humans
About 37
72
What does thermos table mean
can withstand temperatures in excess of 80 °C
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What is the tempo coefficient for a biological reaction
ratio between the rates of that reaction at two different temperatures
74
What is the temp coefficient for most enzyme controlled reaction
• For most enzyme-catalysed reactions the rate of the reaction doubles for every 10 °C increase in temperature
• The temperature coefficient (Q) for a reaction that follows this pattern is: Q₁₀ = 2
75
Formula for temp coefficient
Temperature coefficient = (rate of reaction at (x + 10) °C) ÷ (rate of reaction at x °C)
(bigger over smaller)
76
How does enzyme concentration effect rate of reaction
• The higher the enzyme concentration in a reaction mixture, the greater the number of active sites available and the greater the likelihood of enzyme-substrate complex formation
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How does the initial rate of reaction increase = enzyme conc
• As long as there is sufficient substrate available, the initial rate of reaction increases linearly with enzyme concentration
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Why would the rate of reaction be limited at some point
amount of substrate is limited, at a certain point any further increase in enzyme concentration will not increase the reaction rate as the amount of substrate becomes a limiting factor
79
Graph for enzyme concentration
80
State how substrate concentration effect rate of reaction
• The greater the substrate concentration, the higher the rate of reaction
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Explain why substrate concentration effects rate of reaction
o As the number of substrate molecules increases, the likelihood of enzyme-substrate complex formation increases
82
Why does the graph eventually plateau off - substrate concentration
o If the enzyme concentration remains fixed but the amount of substrate is increased past a certain point, however, all available active sites eventually become saturated and any further increase in substrate concentration will not increase the reaction rate
83
Graph - substrate concentration
84
What is a reversible inhibitor
• Temporarily stops / reduces enzyme activity
85
Two types of reversible inhibitor
competitive + non – competitive
86
What is a competitive inhibitor
similar shape to that of the substrate molecules and therefore compete with the substrate for the active site
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What is a non - competitive inhibitor
bind to the enzyme at an alternative site = alters the shape of the active site and therefore prevents the substrate from binding to it
88
Diagram for competitive inhibition
89
Diagram for non-competitive inhibition
90
How do reversible inhibitors effect reaction rate
• (Non) competitive = both reduce rate of reaction
91
What happens if you increase concentration if inhibitor
reduces rate further = eventually stop the reaction
92
How do you counter an increase in competitive inhibitors
can counter increase in inhibitor concentration by increasing substrate concentration = more substrate molecules mean they are more likely to collide with enzymes and form enzyme-substrate complexes
93
Does the way to counter competitive work for non competitive
No
94
Why does the way to counter competitive not work for non competitive
as the shape of the active site of the enzyme remains changed and enzyme-substrate complexes are still unable to form
95
Does the amount of product change with competitive
NO
96
Why does the amount of product not change with competitive
lower the initial rate of reaction (by occupying some of the available active sites) = eventually same amount of product will be produced as would have been produced without the competitive inhibitor (the maximal rate is not affected)
97
Do non competitive inhibitors lower the amount of product formed
Yes
98
Draw a graph - rate of reaction against substrate concentration - do normal enzyme / competitive inhibitor and non - competitive
99
Describe end product inhibition
o As the enzyme converts the substrate into product, the process is itself slowed down as the end-product of the reaction chain binds to an alternative site on the original enzyme, changing the shape of the active site and preventing the formation of further enzyme-substrate complexes
100
How is the end product inhibitor a negative feedback loop
o The end-product can then detach from the enzyme and be used elsewhere, allowing the active site to reform and the enzyme to return to an active state
o This means that as product levels fall, the enzyme begins catalysing the reaction once again, in a continuous feedback loop
101
What are non reversible inhibitors
• Some inhibitors can form covalent bonds with enzymes, inhibiting them permanently = non-reversible
102
What do non reversible inhibitors result in
complete inactivation of the enzyme
103
Why is non reversible inhibition dangerous
the biological reaction the enzyme is catalysing to be completely stopped
104
How does the cell avoid this danger
the cell or organism to produce more of the enzyme being inhibited
105
Why is producing more of the enzyme not as easy as it sounds
only be achieved by transcribing and translating the gene(s) for that enzyme = relatively slow process
106
What can irreversible inhibitors also be known as
metabolic poisons (as stops metabolic reaction)
107
Example of metabolic poison
Cyanide
108
How does cyanide work
non-reversible inhibitor of cytochrome oxidase, a mitochondrial enzyme that catalyses one of the key reactions in aerobic respiration
can be fatal as it takes too long to produce new enzymes and the organism will die before this can occur
109
Other non reversible inhibitors / metabolic poisons
lead + mercury
110
How does lead work as a non reversible inhibitor
non-reversible inhibitor of ferrochelatase, an enzyme involved in the production of haem for haemoglobin
111
3 Medicinal drugs
Penicillin
Aspirin
Eflornithine
112
How does penicillin work
Non-reversible inhibition of transpeptidase (the enzyme that helps form the cross-Links in bacterial cell walls)
113
How does aspirin work
Non-reversible inhibition of COX = the enzyme that helps produce prostaglandins for stimulating inflammation and pain
114
How does eflorithine work
Non-reversible inhibition of ornithine decarboxylase (an enzyme essential to cell growth)
115
Medical benefit of penicillin
Results in the destruction of bacteria as their cell walls break down
116
Medical benefit of aspirin
Results in the reduction of inflammation and provides pain relief
117
How does eflornithine work
Used in the treatment of sleeping sickens = African trypanosomiasis
118
What are cofactors
• inorganic ions
• non-proteins
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What are cofactors needed for
• enzymes require them to function properly
120
What do cofactors do
• help stabilise the structure of an enzyme or take part in a reaction at active site
121
Example of a cofactor
chloride ions act as a cofactor for amylase
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How do cofactors actually work
• may accept hydrogen ions, electrons or other small molecules that enable the main reaction to occur
123
What are coenzymes
• larger organic cofactors = coenzymes
• non-protein
124
Are co enzymes permanent or temporary
• some = permanently bound to the enzyme = in / near active site
• some = bind temporarily
125
Are cofactors permenatly or temporarily blind
Typically permenantly
126
How do co enzymes work
• often changes the shape of the active site to allow the binding of a substrate
127
Cofactors are from inorganic ions. Where are co enzymes from
• often vitamins / derived from vitamins = especially vitamin B
128
What are co enzymes often involved in
Electron transfer reactions
129
What conenzyme does vitamin B1 produce
coenzyme FAD
130
What is the coenzyme FAD used for
coenzyme required in the Krebs cycle during respiration
131
How are coenzymes used in respiration
• During many of the reactions in respiration, the coenzymes NAD and FAD are alternately reduced and oxidised, transferring energy in the form of hydrogen ions
132
Where is the coenzyme NADP found + used for
Chlorplasts in photosynthesis
133
What is the co enzyme ATP responsible for
the transfer of phosphate groups between respiration and energy-consuming processes in cells
134
What is coenzyme A responsible for
the transfer of an acetyl group (-CH₃CO) from fatty acids and glucose during respiration
135
What are prosthetic groups
• cofactors are actually a permanent part of the structure of the enzyme they assist = prosthetic group
136
Why are prosthetic groups important
• essential to the enzyme functioning properly, as they help to form the final 3D shape of the enzyme
137
How does the prosthetic group zinc work
, by forming part of the active site of the enzyme, a zinc ion acts as the prosthetic group for carbonic anhydrase (an enzyme found in red blood cells that converts CO₂ and H₂O into carbonic acid, H₂CO₃)
138
How to investigate enzyme activity - using water
the rate of product formation is used to measure the rate of an enzyme-controlled reaction:
139
How to investigate enzyme activity using water
o Hydrogen peroxide is a common but toxic by-product of metabolism
o This means it must be broken down quickly
o Catalase is an enzyme found in the cells of most organisms that breaks down hydrogen peroxide into water and oxygen
o Hydrogen peroxide and catalase are combined and the volume of oxygen generated is measured in a set time
o The rate of reaction can then be calculated
140
Cofactor for amylase - spec
Cl-
141
Prosthetic group for carbonic anhydrase
Zn 2+
142
Source of coenzymes - spec
Vitamins
