Enzymes Flashcards
1
Q
define active site
A
- Active site is the 3D region within the enzyme that fits the substrate, the amino acid side chains align to bind to the substrate
2
Q
define substrate specificity
A
enzymes only act on certain substrates
3
Q
define activation energy
A
the minimal amount of energy required for substrates to undergo a chemical reaction
4
Q
describe cofactor
A
this is a non-protein component of an enzyme that is required for activity and for the enzyme to catalyse a reaction but not the substrate itself
5
Q
define coenzyme
A
a dissociable non protein which participates in the enzyme reaction and frequently interacts with multiple enzymes, can act to carry things between enzymes
6
Q
define pro-enzyme
A
This is the inactive form of the enzyme in the cytoplasm before it is active, they can also be called the zymogen
they need to be chemically changed for it to work
7
Q
describe the characteristics of enzymes
A
- Enzymes are protein catalysts
- Increase the rate of a biological reaction by lowering the activation energy, by finding an alternative route that has a lower activation energy
- They catalyse all the chemical reactions taking place in the cells
8
Q
What are the bonds between the enzymes active site and the substrate molecules
A
- Hydrophobic interactions
- Salt bridges
- Hydrogen bonds
9
Q
why are the products release
A
- Products are released when the reaction is complete as they no longer fit into the active site well
10
Q
what will result in the enzyme not working
A
- Mutations that remove the important amino acids or change the shape of the enzyme will result in the enzyme not working
11
Q
name the bonds that bond between the enzymes active site and the substrate
A
hydrogen bonding
salt bridges
hydrophobic interactions
12
Q
describe the lock and key hypothesis
A
- Active site has a rigid shape
- Only substrates that match the shape can fit
- Substrate is a key that fits into the lock of the active site and forms an enzyme susbtrate complex
13
Q
describe the induced fit model
A
- Active site is flexible
- The active site and substrate adjust to maximise the fit which improves catalyst
- There is a greater range of substrate specificity
- Model is more consistent with a wider range of enzymes
14
Q
enzymes may recognise and catalyse a…
A
- single substrate (Absolute)
- group of similar substrates,(group)
- a particular type of bond (linkage)
15
Q
if something has the word -ase in what does this mean
A
means it is an enzyme
e.g. lipase
16
Q
describe how enzymes are named
A
- Can describe the function – oxidases – catalyse oxidation reactions
- Sometimes common names are used for the digestion enzymes such as pepsin and trypsin - these were named before nomenclature were used
- Sometimes the names describe the substrate and function, alcohol dehydrogenase oxidises ethanol
17
Q
what is a prosthetic group
A
non-dissociable cofactor
18
Q
what is a apoenzyme
A
enzyme lacking cofactor (inactive)
19
Q
what is a holoenzyme
A
enzyme with a cofactor (active)
20
Q
why do enzymes use cofactors and coenzymes
A
- they use these things and metal ions in order to gain multiple oxidations states as they cannot do this with oxygen
21
Q
describe Heme as an example of an cofactor
A
- Heme is a common enzyme co factor
- Porphyrin ring containing iron
- Present in many enzymes involved in oxidation reactions for example
- Myeloperoxidase, Cyt C oxidase glutathione oxidase all contain heme as an essential cofactor
22
Q
naem an example of a cofactor
A
Heme
23
Q
name an example of a coenzyme
A
NAD
24
Q
describe the function of NAD
A
- This is involved in moving electrons between enzymes
- Important in oxidation and reduction reactions
- Can exist in both oxidised and reduced forms therefore is able to carry electrons in both these directions
25
what is a vitamin
this is a required micro-nutrient, the organism cannot synthesize adequate quantities for normal health,
26
why does the body fail without vitamins
- Without vitamins and minerals body fails to function because they make the cofactors and conezymes
27
what are diseases associated with vitamin deficiency
- Beri-Beria deficiency in B1
- scurvey - deficiency in vitamin C
- pellagra - deficiency in vitamime B3
28
Name the different classes of enzymes
- oxidoreductases
- transferases
- hydrolases
- lyases
- isomerases
- ligases
29
what does oxidoreductases do
- oxidation reduction reactions
30
what does transferase do
- transfer of functional groups such as amino, phosphate and methyl
31
what does hydrolyses do
- hydrolysis such as peptide and ester bonds
32
what does lyases do
- adds atoms/removes atoms to and from a double bond such ad carbon dioxide ammonia
33
what does isomerases do
rearrange atoms
Cis trans isomers
DL isomers in sugars
34
what does ligases do
use ATP to combine molecules such as link reaction which adds carbon dioxide
35
most enzymes are synthesised in ...
in an inactive form, this is called the zymogen or proenzyme
36
why do you want the enzyme in an inactive form (proenzyme)
- Don’t want to be active inside the cytoplasm, therefore instead body makes proenzymes so for example digestion enzymes would digest the cell
37
how do you activate an proenzyme
- Activation usually requires proteolytic conversion of the proenzyme
- Not reversible: activation occurs once in the life of the enzyme, this is because it is usually cleavage
38
give some examples of an proenzyme
- Digestive enzymes, blood clotting enzymes, complement, developmental enzymes
39
name an example of a proenzyme
- chymotyrpsinogen
40
where is chymotrypsingoen
- made
- stored
- Made in the pancreases in acinar cells
| - Stored in membrane bound granules – acinar cells
41
what does chymotrypsinogen do
- Stimulates the release to duodenum
- Single polypeptide chain of 245 amino acid residues – inactive proenzyme
- Requires activation in the lumen to produce active enzyme
- Cleaves peptide bonds containing aromatic amino acids
42
how is chymotrypsinogen activated
- Two step activation process
- Cleaved peptide bond between Arg-15 and lle -16 by trypsin to generate dipeptide
- Pie chymotrypsin is active
- Pie chymotrypsin acts on other pie-chymotrypsin molecules
- Two dipeptides removed to generate final active enzyme which is alpha chymotrypsin
- They are 3 chains interconnected by disulphide bonds
- 2 dipeptides are removed – (dipeptide 14 and 15 and dipeptide 147 and 148)
43
what is trypsin
- It is the common activator of all the pancreatic proenzymes
44
describe temperature and activity
- Enzymes are most active at an optimum temperature
- Show little activity at low temperatures
- Activity is lost at high temperature as denature occurs
- hydrogen bonds break the peptide chain in the enzymes
45
describe pH and activity
- Enzymes most active at optimum pH
- Amino acids with acidic or basic side chains have the appropriate charges for functional enzyme activity when the pH is optimum
- Activity is lost when tertiary structure is disrupted
- Optimum pH is normally the pH where the enzyme is required to act
- hydrogen and ionic bonding of the peptides make the enzymes hold its shape - these is affected by pH
46
describe enzyme concentration
- The rate of reaction increases as enzyme concentration increases
- At higher enzyme concentrations more enzymes are available to catalyse the reaction
- There is a linear relationship between the reaction rate and enzyme concentration
47
describe substrate concentration
- Rate of reaction increases as substrate concentration increases
- Maximum activity occurs when all enzymes are binding to a susbtrate
- The relationship between reaction rate and substrate concentration is exponential and asymptotes when the enzyme is saturated
48
what is an inhibitor
- Enzyme inhibitors are molecules that cause a loss of enzyme activity as they prevent substrates from fitting into the active site of the enzyme
- prevent the substrate from fitting into the active site of the enzyme
49
How do competitive inhibitors work?
- A competitive inhibitor has a structure like the substrate it competes with the substrate for the active site
- A competitive inhibitor can be reversible or irreversible
- In the case of a reversible inhibitor it is the effect is reversed by increasing the substrate concentration
- In the case of an irreversible inhibitor it remains chemically bound in the active site
50
How do reversible competitive inhibitors work
- Malonate – this is an competitive inhibitor of succinate dehydrogenase, it has a structure that is similar to succinate
- Inhibition can be reversed by adding excess succinate
- Other examples of competitive inhibitors: HIV-1 aspartyl protease inhibitor and reverse transcriptase inhibitors of HIV and other retroviruses
51
how do irreversible inhibitors work
- This destroys enzymes activity by bonding with side chain groups in the active site
- This is a chemical reaction and is time dependent
52
How do non-competitive inhibitors work
- A non-competitive inhibitor has a structure that is different than that of the substrate
- It binds to the allosteric site rather than to the active site
- It changes the shape of the enzyme which alters the shape of the active site and prevents the binding of the substrate
- The effect cannot be reversed by adding more substrate as they are effecting the shape of the active site
- The effect is reversed when the concentration of the inhibitor falls
53
How do uncompetitive inhibitors work
- It binds to the enzyme substrate complex prevents the reaction from completing
- The effect increases by adding more substrate
- The effect is reversed when the concentration of the inhibitor falls
54
what is an un-compeitive inhibitor
an uncompetitive inhibitor has a structure that is different from that of a substrate and binds to the enzyme substrate complex therefore preventing the reaction from completing
55
give some examples of irreversible inhibitors
cyanide
sarin
penicillin
56
non-competitive feedback inhibition
- further down the pathway turns an enzyme off further up the pathway
57
what are Iso-enzymes
these are different forms of an enzyme that catalyse the same reaction in different tissues of the body
- they have different gene products and have different kinetic properties
58
give an example of an Isoenzymes
- Lactate dehydrogenase (LDH) converts lactate to pyruvate consists of five isoenzymes
- H form heart tissue
- M form muscle tissue
- quaternary structure made from 4 subunits which has different combinations of H and M subunits
59
why are isoenzymes different
- Gene product
- Kinetic properties
- Variation in amino acid sequences of subunits (in quaternary structure)
- Different gene products and different kinetic properties
60
what are roles of diagnostic enzymes
- The levels of diagnostic enzymes in the blood can be used to determine the amount of damage in specific tissues
- In the whole the blood does not contain enzymes but when the tissue is damage they are released into the blood
- Measure the enzymes and this tells us information about what is damaged
- Serum enzymes are used in the diagnosis
61
what are the 3 types of specificities
1. absolute - enzyme only acts on one substrate
2. group - enzyme only acts on a group/family of chemicals
3. linkage - enzyme acts on one type of reaction for example the substrate is a specific type of bond such as peptide bonds
62
name some examples of pro-enzymes and there active enzymes
```
pepsinogen - pepsin
chymotrypsinogen - chymotrypsin
trypsinogen - trypsin
procarboxypeptidase - carboxypeptidsase
proelastase - elastase
```
63
what is the Vmax
this is when eventually increasing the substrate concentration will no longer have any effects as the enzymes are all saturated as they are all filled with substrate this is the Vmax
64
what does the Km tell you
this tells you at what concentration of substrate the reaction is half of the maximum
65
what does High Km mean
this means the enzyme has a low affinity for a substrate therefore a low rate of reaction
66
what does a low Km mean
this means the enzyme has a high affinity for a substrate therefore it has a high rate of reaction
67
Give examples of reverssible competitive inhibitors
Malonate
HIV 1 aspartyl protease inhibitors
Reverse transcriptase inhibitors of HIV
68
What are the examples of NAD
- Lactate dehydrogenase
| - Glyceraldehye -3-phosphate dehydrogenase in glycolysis
69
What are vitamins precursors off
precursors of co-factors and co-enzyme
70
What are the types of inhibitors
- Competitive inhibitors – reversible and irreversible
- Non-competitive inhibitors
- Un-competitive inhibitors
71
why does the rate slow down in uncompetitive inhibitors
- Actual rate – less product formed
| - Apparent rate- slow ES dissociation
72
what do isoenzymes permit
they permit fine tuning of metabolism
