Enzymes Flashcards
define active site
- Active site is the 3D region within the enzyme that fits the substrate, the amino acid side chains align to bind to the substrate
define substrate specificity
enzymes only act on certain substrates
define activation energy
the minimal amount of energy required for substrates to undergo a chemical reaction
describe cofactor
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
define coenzyme
a dissociable non protein which participates in the enzyme reaction and frequently interacts with multiple enzymes, can act to carry things between enzymes
define pro-enzyme
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
describe the characteristics of enzymes
- 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
What are the bonds between the enzymes active site and the substrate molecules
- Hydrophobic interactions
- Salt bridges
- Hydrogen bonds
why are the products release
- Products are released when the reaction is complete as they no longer fit into the active site well
what will result in the enzyme not working
- Mutations that remove the important amino acids or change the shape of the enzyme will result in the enzyme not working
name the bonds that bond between the enzymes active site and the substrate
hydrogen bonding
salt bridges
hydrophobic interactions
describe the lock and key hypothesis
- 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
describe the induced fit model
- 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
enzymes may recognise and catalyse a…
- single substrate (Absolute)
- group of similar substrates,(group)
- a particular type of bond (linkage)
if something has the word -ase in what does this mean
means it is an enzyme
e.g. lipase
describe how enzymes are named
- 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
what is a prosthetic group
non-dissociable cofactor
what is a apoenzyme
enzyme lacking cofactor (inactive)
what is a holoenzyme
enzyme with a cofactor (active)
why do enzymes use cofactors and coenzymes
- they use these things and metal ions in order to gain multiple oxidations states as they cannot do this with oxygen
describe Heme as an example of an cofactor
- 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
naem an example of a cofactor
Heme
name an example of a coenzyme
NAD
describe the function of NAD
- 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
what is a vitamin
this is a required micro-nutrient, the organism cannot synthesize adequate quantities for normal health,
why does the body fail without vitamins
- Without vitamins and minerals body fails to function because they make the cofactors and conezymes
what are diseases associated with vitamin deficiency
- Beri-Beria deficiency in B1
- scurvey - deficiency in vitamin C
- pellagra - deficiency in vitamime B3
Name the different classes of enzymes
- oxidoreductases
- transferases
- hydrolases
- lyases
- isomerases
- ligases
what does oxidoreductases do
- oxidation reduction reactions
what does transferase do
- transfer of functional groups such as amino, phosphate and methyl
what does hydrolyses do
- hydrolysis such as peptide and ester bonds
what does lyases do
- adds atoms/removes atoms to and from a double bond such ad carbon dioxide ammonia
what does isomerases do
rearrange atoms
Cis trans isomers
DL isomers in sugars
what does ligases do
use ATP to combine molecules such as link reaction which adds carbon dioxide
most enzymes are synthesised in …
in an inactive form, this is called the zymogen or proenzyme
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
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
give some examples of an proenzyme
- Digestive enzymes, blood clotting enzymes, complement, developmental enzymes
name an example of a proenzyme
- chymotyrpsinogen
where is chymotrypsingoen
- made
- stored
- Made in the pancreases in acinar cells
- Stored in membrane bound granules – acinar cells
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
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)
what is trypsin
- It is the common activator of all the pancreatic proenzymes
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
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
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
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
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
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
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
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
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
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
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
give some examples of irreversible inhibitors
cyanide
sarin
penicillin
non-competitive feedback inhibition
- further down the pathway turns an enzyme off further up the pathway
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
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
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
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
what are the 3 types of specificities
- absolute - enzyme only acts on one substrate
- group - enzyme only acts on a group/family of chemicals
- linkage - enzyme acts on one type of reaction for example the substrate is a specific type of bond such as peptide bonds
name some examples of pro-enzymes and there active enzymes
pepsinogen - pepsin chymotrypsinogen - chymotrypsin trypsinogen - trypsin procarboxypeptidase - carboxypeptidsase proelastase - elastase
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
what does the Km tell you
this tells you at what concentration of substrate the reaction is half of the maximum
what does High Km mean
this means the enzyme has a low affinity for a substrate therefore a low rate of reaction
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
Give examples of reverssible competitive inhibitors
Malonate
HIV 1 aspartyl protease inhibitors
Reverse transcriptase inhibitors of HIV
What are the examples of NAD
- Lactate dehydrogenase
- Glyceraldehye -3-phosphate dehydrogenase in glycolysis
What are vitamins precursors off
precursors of co-factors and co-enzyme
What are the types of inhibitors
- Competitive inhibitors – reversible and irreversible
- Non-competitive inhibitors
- Un-competitive inhibitors
why does the rate slow down in uncompetitive inhibitors
- Actual rate – less product formed
- Apparent rate- slow ES dissociation
what do isoenzymes permit
they permit fine tuning of metabolism
