enzymes Flashcards
1
Q
What are enzymes?
A
Biological catalysts that interact with
substrate molecules to facilitate
chemical reactions. Usually globular
proteins
2
Q
Why are enzymes
important?
A
The allow reactions to happen quickly without extreme conditions (e.g. high temperatures and pressures) that are not possible in living cells because they would damage the cell components
3
Q
What is a substrate?
A
A substance used, or acted on, by
another process or substance, e.g. a
reactant in an enzyme-catalysed
reaction
4
Q
What is anabolism?
A
Anabolic reactions of metabolism that construct molecules from smaller units. These reactions require energy from the hydrolysis of ATP, and are catalysed by enzymes
5
Q
What is catabolism?
A
Catabolic reactions of metabolism that break molecules down into smaller units. These reactions release energy, and are catalysed by enzymes
6
Q
What is metabolism?
A
The sum of all of the different
reactions and reaction pathways
happening in a cell or organism
7
Q
What is meant by ‘Vmax’?
A
Maximum initial velocity or rate of an
enzyme-catalysed reaction
8
Q
Describe the mechanism of
enzyme action
A
Enzymes help the molecules collide
successfully, and therefore reduce
the activation energy required
9
Q
What is the active site of an
enzyme?
A
An area within the tertiary structure of the enzyme that has a shape that is complementary to the shape of a specific substrate molecule. This allows the enzyme to bind to a substrate with specificity
10
Q
What is the ‘Lock and Key
Hypothesis’ of enzyme
action?
A
In the same way that only the right key will fit into a lock, only a specific substrate will ‘fit’ the active site of an enzyme Enzyme + Substrate —> ESC —> Enzymes + Products
11
Q
How does the enzyme act
on the substrate in the Lock
and Key Hypothesis?
A
• The substrate and enzyme molecules each have KE and are constantly moving randomly • If a substrate molecule successfully collides with an enzyme molecule, an ESC forms • The substrate is held in such a way by the enzyme that the right atom-groups are close enough to react • The R-groups within the active site of the enzyme will also interact with the substrate forming temporary bonds • These put strain on the bonds within the substrate, which also helps the reaction along • The substrate is converted into the product, an EPC formed, and then the products leave the enzyme
12
Q
What is the ‘Induced Fit
Hypothesis’?
A
Modified lock and key explanation
for enzyme action: the active site of
the enzyme is modified in shape by
binding to the substrate
13
Q
How does the enzyme act
on the substrate in the
Induced Fit Hypothesis?
A
• The active site of the enzyme changes shape slightly as the substrate enters to fit it better • An ESC is formed, and noncovalent R-group interactions (e.g. hydrogen bonds, ionic attractions, van Der Waals forces and hydrophobic interactions) bind the substrate molecule to the enzyme’s active site • This can weaken bonds in the substrate, lowering the activation energy for the reaction • The substrate is converted into the product forming an EPC • As the product molecules have a slightly different shape from the substrate molecule, they detach from the active site
14
Q
What are intracellular
enzymes? (Give an example)
A
Enzymes that act within cells • Hydrogen peroxide is a toxic product of many metabolic pathways • Enzyme catalase break it down into O2 and H2O quickly, preventing its accumulation • Found in both animal and plant tissues
15
Q
What are extracellular
enzymes?
A
Enzymes that act outside the cell that made them (in some organisms e.g. fungi, they work outside the body) • The substrates for intracellular enzymes (e.g. nutrients) are large molecules that can’t enter the cell directly though the cell membrane • Extracellular enzymes are released from cells to break down the large nutrient molecules into smaller molecules in the process of digestion
16
Q
Describe the process of the
digestion of starch
A
1. Starch polymers are broken down into maltose (disaccharide) by amylase which is produced by the salivary glands and the pancreas. It’s released in saliva into the mouth, and in pancreatic juice into the small intestine 2. Maltose is broken down into glucose (monosaccharide) by maltase in the small intestine
17
Q
Describe the process of the
digestion of proteins
A
Trypsin is a protease that catalyses the digestion of proteins into smaller peptides which can be broken further into amino acids by other proteases • It’s produced in the pancreas and released with the pancreatic juice into the small intestine, where it acts on proteins
18
Q
Why does increasing the
temperature initial increase
the rate of reaction?
A
If a reactant mixture containing enzyme and substrate molecules is heated: • Both types of molecule will gain KE and move faster • This will increase the rate of successful collision • The rate of formation of ESCs increases and the rate of reaction increases, increasing the number of EPCs per second, up to a point
19
Q
What is a enzyme’s optimum
temperature?
A
The temperature at which the enzyme has the highest rate of activity • Around 40˚C in humans • 70˚C for thermophilic bacteria • Below 5˚C for psychrophilic organisms
20
Q
What does denaturation
mean?
A
Change in the tertiary structure of a
protein or enzyme, resulting in loss
of normal function
21
Q
What happens when the
temperature is increased
past the optimum?
A
Increasing temperature makes molecules vibrate • This may break some of the weak bonds (e.g. hydrogen and ionic bonds) that hold the tertiary structure of the enzyme’s active site • As the active site shape begins to change, the substrate won’t fit in so well, and the rate of reaction begins to decrease • As more heat is applied, the active site completely and irreversibly changes so that it is no longer complementary to the substrate • The reaction can’t proceed at all • The enzyme is denatures • (primary structure is not altered as heat doesn’t break peptide bonds)
22
Q
What is the temperature
coefficient, Q10?
A
A measure of how much the rate of reaction increases with a 10˚C temperature increase. Usually taken as 2 for enzymecontrolled reactions i.e rate of reaction doubles with 10˚C increase
23
Q
Why does pH affect
enzymes?
A
• A change in pH refers to a change in hydrogen ion concentration • Active site is only the right shape at a certain hydrogen ion concentration • Hydrogen bonds and ionic bonds between amino acid R-groups hold proteins in their precise 3D shapes • Hydrogen ions interact with polar and charged R-groups, affecting the interaction of the R-groups with each other • The more hydrogen ions present (low pH) the less R-groups can interact with each other leading to bonds breaking and the shape of the enzyme changing. The reverse is true when less hydrogen ions present (high pH) • Shape of enzyme will change, so it can only function within a narrow pH range
24
Q
Why do enzymes only work
within a narrow pH range?
A
Small changes of pH either side of the optimum slow ROR because the shape of the active site is disrupted • If normal optimum pH is restored, the hydrogen bonds can reformat the active site’s shape is restored • At extremes of pH, the active site may be permanently changed; the enzyme is denatured
25
What happens when the
concentration of substrate
is increased?
```
• Higher collision rate, so the rate of
reaction increases
• Leads to the formation of ESCs at
a faster rate
• The rate of reaction increases up
to its maximum (Vmax) - at this
point all of the active sites are
occupied and no more ESCs can
be formed until products are
released from active sites
• The only way to increase the ROR
would be to add more enzyme or
increase the temperature
• If the concentration of enzyme is
increased, more active sites are
available so the ROR can rise
towards a higher Vmax.
```
26
What is an inhibitor?
```
A factor that prevents or reduces the
rate of an enzyme-catalysed
reaction.
There are 2 types: competitive and
non-non-competitive
```
27
What is a competitive
| inhibitor?
An inhibitor that competes with
substrate to bind to active site on an
enzyme
28
How does competitive
| inhibition work?
```
1. A molecule or part of a molecule
that has a similar shape to the
substrate of an enzyme can fit
into the active site of the enzyme
2. This blocks the substrate from
entering the active site,
preventing the enzyme from
catalysing the reaction
3. The enzyme cannot carry out its
function and is said to inhibited
```
29
What is the effect of
| competitive inhibition?
```
• Substrate and inhibitor molecules
present in a solution will compete
with each other to bind to the
active sites of the enzymes
catalysing the reaction
• The rescues the number of
substrate molecules binding to
active sites in a given time and
slows down the rate of reaction
• Degree of inhibition will depend on
the relative concentrations of
substrate, inhibitor, and enzyme
• Most competitive inhibitors only
bind temporarily to the active site
```
30
What is the effect of a
competitive inhibitor on rate
of reaction?
```
• Reduces the rate of reaction for a
given concentration of substrate
• Doesn’t change the Vmax of the
enzyme
• If substrate concentration is
increased, there will be so much
more substrate than the inhibitor
that the original Vmax can still be
reached
```
31
Give 2 examples of
| competitive inhibitiors
```
Statins
• Competitive inhibitors of an
enzyme used in cholesterol
synthesis
• Prescribed to help people reduce
blood cholesterol concentration
• High blood cholesterol levels can
result in heart disease
Aspirin
• Irreversibly inhibits the active site
of COX enzymes, preventing the
synthesis of prostaglandins and
thromboxane, the chemicals
responsible for producing pain and
fever
```
32
What is a non-competitive
| inhibitor?
A inhibitor that binds to an enzyme
| at an allosteric site
33
How does non-competitive
| inhibition work?
```
• Inhibitor binds to the enzyme at a
location other than the active site.
This alternative sites called an
allosteric site
• Binding of the inhibitor causes the
tertiary structure of the enzyme to
change, meaning the active site
changes shape
• Active site no longer has
complementary shape to
substrate, so its is unable to bind
to the enzyme
• Enzyme cannot carry out its
function and is said to be inhibited
```
34
What is the effect of a noncompetitive inhibitor on rate
| of reaction?
```
• Increasing concentration of
enzyme or substrate will not
overcome the effect of a noncompetitive inhibitor
• Increasing the concentration of
inhibitor will decrease rate of
reaction further as more active
sites become unavailable
• Lower Vmax
```
35
Give examples of
irreversible non-competitive
inhibitors
```
Organophosphates
• Used as insecticides and
herbicides
• Irreversibly inhibit the enzyme
acetyl cholinesterase (necessary
for nerve impulse transmission)
• Can lead to muscle cramps,
paralysis and death if ingested
Protein Pump Inhibitors (PPI)
• Used to treat long-term indigestion
• Irreversibly block an enzyme
system responsible for secreting
hydrogen ions into the stomach
• Makes PPIs very effective in
reducing the production of excess
acid which, if left untreated, can
lead to the formation of stomach
ulcers
```
36
What is end-product
| inhibition?
```
The product of a reaction inhibits the
enzyme required for the reaction.
• Negative-feedback control
mechanism for the reaction
• Excess products are not made and
resources are not wasted
• Example of non-non-competitive
reversible inhibition
```
37
Describe the metabolic
| pathway of respiration
```
• Results in the production of ATP
• Glucose is broken down
• Addition of 2 phosphate groups to
glucose molecule
• The addition of the 2nd phosphate
group results in the initial
breakdown of the glucose
molecule, and is catalysed by the
enzyme phosphofructokinase
(PFK)
• This enzyme is competitively
inhibited by ATP
• Therefore ATP regulates its own
production
```
38
Describe how ATP regulates
| its own production
```
When ATP levels are high…
• More ATP binds to the allosteric
site of PFK, preventing the
addition of the 2nd phosphate
group to glucose
• Glucose is not broken down, and
ATP is not produced at the same
rate
As ATP is used up…
• Less binds to PFK
• PFK is able to catalyse the
addition of the 2nd phosphate
group to glucose
• Respiration resumes, leading the
the production of more ATP
```
39
What are cofactors needed
| for?
```
Needed by enzymes in order to
carry out their function as
biological catalysts
• May transfer atom groups from
one reaction to another in a multistep pathway
• May form part of the active site of
an enzyme
```
40
What is a cofactor?
```
Non-protein components necessary
for the effective functioning of an
enzyme
Inorganic cofactors:
• Obtained via the diet as minerals,
including iron, calcium, chloride
and zinc ions
• e.g. Amylase contains a chloride
ion that is necessary for the
formation of a correctly shaped
active site
```
41
What is a coenzyme?
```
An organic cofactor
• Derived from vitamins
• e.g. vitamin B3 is used to
synthesise NAD (nicotinamide
adenine dinucleotide), a coenzyme
responsible for the transfer of
hydrogen atoms between
molecules involved in respiration
• e.g. vitamin B5 is used to make
Coenzyme A, which is essential in
the breakdown of fatty acids and
carbohydrates in respiration
```
42
How are prosthetic groups
| different to other cofactors?
```
Prosthetic groups are cofactors
required by certain enzymes to carry
out their catalytic function
• Some cofactors are loosely or
temporarily bound to the enzyme
protein in order to activate them,
but prosthetic groups are tightly
bound and form a permanent
feature of the protein
• e.g. Zn2+ ions form an important
part of the structure of carbonic
anhydrase, an enzyme necessary
for the breakdown of CO2
```
43
What are inactive precursor
| enzymes?
```
• Enzymes produces in a inactive
form
• Esp. enzymes that can cause
damage within the cells producing
them or tissues where they are
released
• OR enzymes whose action needs
to be controlled and only activated
under certain conditions
```
44
How do precursor enzymes
| work?
```
• They need to undergo a change in
shape (tertiary structure), esp.to
the active site to be activated
• This happens with the addition of
a cofactor
• Before the cofactor is added, the
precursor protein is called an
apoenzyme
• When the cofactor is added and
the enzyme activated, it is called a
holoenzyme
```
45
How else can the change in
tertiary structure be brought
about?
```
• The action of another enzyme, e.g.
protease, which cleaves certain
bonds in the molecule
• A change in conditions e.g. pH or
temperature can result in a change
in tertiary structure and activate a
precursor enzyme
• These types of precursor enzymes
are called zymogens or
proenzymes
```
46
Give an example of
| precursor activation
```
• When inactive pepsinogen is
released into the stomach to
digest proteins,acid pH transforms
it into the active enzyme pepsin
• This adaptation protects body
tissues against the digestive action
of pepsin
```
