Enzymes Flashcards
What are ENZYMES?
BIOLOGICAL CATALYSTS:
- Increase the rate of reactions
- Found in living organisms
CATALYSE BOTH:
Anabolic reactions ~ building up
Catabolic reactions ~ breaking down
The STRUCTURE of enzymes
- TERTIARY GLOBULAR proteins, where the protein chain is folded back on itself into a SPHERICAL shape.
- Each enzymes has its own sequence of AMINO ACIDS and is held in its tertiary structure by HYDROGEN, IONIC & DISULFIDE bonds.
- On the surface, the tertiary structure of the enzyme folds into a 3D shape called the ACTIVE SITE.
The PROPERTIES of enzymes
SOLUBLE IN WATER ~ have hydrophilic amino acids on their surface and the hydrophobic ones cluster together.
SPECIFIC ~ the tertiary structure of the active site is COMPLEMENTARY to the structure of the substrate.
HIGH TURN OVER NUMBER ~ can convert many molecules of substrate per unit time.
INTRACELLULAR enzymes
Found INSIDE cells.
CATALASE:
Binds to the toxic molecule HYDROGEN PEROXIDE and speeds up its break down in to the harmless products water and oxygen
hydrogen peroxide ———— water + oxygen
catalase
DNA REPLICATION:
- DNA polymerase
- DNA ligase
ON A MEMBRANE:
- The synthesis of ATP by ATPase during respiration
- occurs across the inner membrane of mitochondria.
EXTRACELLULAR enzymes
Found OUTSIDE of cells.
AMYLASE:
- Catalyses the break down of STARCH molecules into the disaccharide MALTOSE.
- Maltose is broken down further by other enzymes into GLUCOSE which can be absorbed into the bloodstream.
Starch ————- maltose
amylase
TRYSPIN:
- Produced by the pancreas and released in the digestive system.
- Catalyses the break down of PROTEIN molecules into PEPTIDES.
- Peptides are broken down into AMINO ACIDS.
Proteins ————————— Peptides
tryspin
How do enzymes work?
- On the surface of an enzyme is the ACTIVE SITE.
- Its role is attach to the SUBSTRATE molecule to form the ENZYME-SUBSTRATE COMPLEX.
- Each enzyme is SPECIFIC to the substrate it binds to.
- Once the substrate binds, the amino acids on the surface of the active site form TEMPORARY BONDS with the substrate molecule.
- The enzymes CATALYSES the reaction to form the ENZYME-PRODUCT COMPLEX.
- Now the products are RELEASED from the active site.
How do enzymes INCREASE THE RATE OF REACTION?
- Provide a PATHWAY for the reaction with a LOWER ACTIVATION ENERGY BARRIER.
- More substrate molecules now have enough energy to cross the activation energy barrier and react.
- Therefore the reaction rate increases.
LOCK & KEY HYPOTHESIS
Fisher 1894:
The substrate is EXACTLY complementary to the shape of the active site.
NATURE OF BINDING:
- Very strong as it does not form a transition state.
ACTIVE SITE PROPERTIES:
- Rigid
- Inflexible
- Static
EVIDENCE:
- Explains the specificity of some enzymes
- Example ~ amylase will only hydrolyse starch
INDUCED FIT HYPOTHESIS
Koshland 1959:
- Interaction of substrate at active site causes CONFORMATIONAL CHANGE .
- This causes the active site to MOULD itself tightly around the substrate.
- Ensures that the active site fits PERFECTLY to the substrate.
- This puts STRAIN on the substrate and weakens bonds.
- Involves a TRANSITIONAL STATE before bonds in the substrate are broken and products are released.
NATURE OF BINDING:
- Flexible, favouring the formation of a transition state.
ACTIVE SITE PROPERTIES:
- Flexible
- Not static
- Dynamic
EVIDENCE:
- Explains broader specificity of some enzymes.
- Example ~ proteins
SIMILARITIES between the two model of the enzyme
- Require an enzyme and a substrate.
- Explain substrate specificity of enzymes
What happens if molecules which are NOT substrate molecules try to bind to the active site?
- Molecules which are not the substrate cannot form the CORRECT BONDS to the correct amino acids int he active site.
- The tertiary structure of the enzyme DOES NOT CHANGE
- The shape of the active site DOES NOT ADJUST to fit the molecule.
Explain the shape of the graph showing the AMOUNT OF PRODUCT FORMED.
In terms of :
- Rate of reaction
- Number of successful collisions
Start:
- Line is STEEP
- LARGE amount of substrate molecules
- High FREQUENCY of successful collisions between the S & AS.
- RAPID initial rate
Middle:
- The line becomes LESS STEEP
- Some of the substrate is CONVERTED into product.
- The amount of substrate molecules FALLS.
- The chance of collision DECREASES
- Reactions SLOWS DOWN
End:
- Line is HORIZONTAL
- ALL of the substrate molecules have been converted into product.
- There are no more substrate molecules left to collide with the active site.
- Reaction has STOPPED
Measuring the rate of reaction at a CERTAIN POINT
- Draw a TANGENT to the curve
- This is a straight line which just touches the curve at the point we want to measure.
- Make the tangent line reasonably long as it makes it easier to read the number accurately.
GRADIENT OF THE TANGENT:
- make the tangent into a TRIANGLE
- measure the length of Y & X
Gradient ( rate ) = Y/X
TEMPERATURE ~ Beginning of reaction
- The rate INCREASES as we INCREASE the temperature.
- The KINETIC ENRGY of the enzyme and substrate INCREASES.
- They are moving more RAPIDLY
- This INCREASES the chance of S & AS colliding.
- The FREQUENCY of successful collisions INCREASE.
- The rate of reaction INCREASES
TEMPERATURE ~ At optimum temperature
- At a certain point, the reaction rate is at its MAXIMUM. (optimum temperature)
- Maximum frequency of collision between S & AS.
Human enzymes optimum temp ~ 40
TEMPERATURE ~ Above optimum temperature
- The rate of reaction DECREASES
- The enzymes are VIBRATING more rapidly.
- This cause the disulfide , hydrogen and ionic BONDS to BREAK.
- The TERTAIRY structure of the enzyme begins to CHANGE.
- As the shape of the active site changes, it is NO LONGER COMPLEMENTARY to the substrate.
- Substrate can no longer fit into the active site.
- The enzyme has DENATURED ~ no longer functions
Can an enzyme renature if we cool it back down?
NO
- The tertiary structure has changed so much.
- Cannot be REVERSED
Temperature coefficient
Shows the rate of reaction at the HIGHER temperature , DIVIDED by the rate of reaction at the LOWER temperature.
Temperature =
coefficient (Q10)
Rate of reaction at temp X + 10 degrees /
Rate of reaction at temperature X
RESULTS of the temperature coefficient
If we increase the temperature by 10 degrees :
- the rate of an enzyme controlled reaction DOUBLES.
- Q10 usually has a value of TWO
- Does not apply above the optimum temperature as the enzymes denature.
The pH of a solution depends on …
- The concentration of HYDROGEN IONS
LOW pH ~ high concentration of H+ e.g pH2
HIGH pH ~ low concentration of H+ e.g pH6
Optimum pH and examples
- Different enzymes work best at different optimum pH
- If the pH changes AWAY from the optimum, the rate of reaction DECREASES
Examples:
pH7 ~ SALIVARY AMYLASE works in the mouth.
pH 2 ~ enzyme that works in an acidic environment e.g stomach
What occurs when H + ions bond with the R groups of the AMINO ACIDS within the active site?
- These amino acids form TEMPORARY BONDS to the substrate
- The action of the H+ PREVENTS these R groups from bonding with the SUBSTRATE
- This REDUCES how effectively the substrate binds to the active site
- This reduce the RATE OF REACTION
What occurs when H+ ions bond with the R groups on amino acids in the rest of the enzyme molecule?
- The BONDS holding the tertiary structure of the enzyme in place are BROKEN.
- This can change the shape of the active site
- makes it less likely that the substrate will attach successfully
- If the pH changes SIGNIFICANTLY then the active site may change shape so much
- It will no longer be COMPLEMENTARY to the substrate ~ DENATURED
The effect of SUBSTRATE CONCENTRATION on the rate of an enzyme-catalysed reaction
- The rate of an enzyme-catalysed reaction is DIRECTLY PROPRTIONAL to the substrate concentration
- LOW substrate concentration = low frequency of collisions between the substrate and active site, rate of reaction is low.
What occurs if we continue to increase the substrate concentration?
- There comes a point where the rate STOPS INCREASING any further.
- At this point , the enzyme is working at its FASTEST RATE ( Vmax)
- At any given time EVERY active site will be colliding with a substrate molecule.
- If we add more substrate then there are NO FREE ACTIVE SITES for the extra substrate molecules to collide with.
- Any increase in the SC will NOT increase the rate of reaction any further
- The enzyme is SATURATED
The effect of ENZYME CONCENTRATION on the rate of an enzyme-catalysed reaction?
- The rate is DIRECTLY PROPORTIONAL to the EC provided that there is MORE SUBSTARTE than enzyme.
DOUBLE EC =
- double the number of active sites
- means double the number of collisions
between active site and substrate
- doubled rate of reaction
The rate of reaction when the EC is LOW and SC is HIGH
- All of the active sites will be colliding with substrate molecules ALL the time
- At any time , a larger number of substrate molecules will be UNABLE to collide with a free active site.
- Rate of reaction will be LOW
What happens if the amount of SUBSTARTE becomes LIMITED?
- Increasing the EC further will no longer increase the rate
- There will not be enough substrate molecules to collide with all the available active sites.
Competitive inhibitor
- A SIMILAR but NOT identical structure to the substrate.
- Competes with the substrate molecule for the active site.
- It is able to BIND to the active site but NO REACTION occurs
- After a short time , the molecule LEAVES the active site.
The EFFECT of a competitive inhibitor
- It occupies the active site for a SHORT IME which PREVENTS the ACTUAL SUBSTARTE from colliding with the active site.
- It REDUCES the rate of reaction
How do we REDUCE the effect of competitive inhibitors?
- INCREASE the concentration of the
SUBSTRATE whilst keeping the competitive inhibitor concentration the SAME. - Much GREATER chance that the substrate will occupy the active site rather than competitive inhibitor
REVERSIBLE Vs IRREVERSIBLE competitive inhibitors
METHOTREXATE: ( reversible)
- used to treat certain cancers
- TEMPORARILY binds to the active site of
enzymes.
PENICILIN: (irreversible)
- involved in the synthesis of bacterial cell
walls. - used to treat bacterial infections.
- PERMANENTLY binds
- Its effect CANNOT be reduced by increasing substrate concentration
Non-competitive inhibitors
- DOES NOT have a similar structure to the substrate.
- This means it DOES NOT bind to the active site of an enzyme
- Instead, binds to a different site on the enzyme molecule called the ALLOSTERIC SITE
Can the effect of a NON-COMPETITIVE INHIBITOR be overcome by increasing the substrate concentration?
NO:
- When the NCI binds tot he allosteric site it causes the TERTIARY STRUCTURE of the enzyme to change
- The SHAPE of the ACTIVE SITE changes so it is no longer complementary to the substrate
- The substrate molecules CANNOT bind to the active site to form the E-Z complex.
- The rate of reaction is REDUCED
Enzyme inhibition
- Plays a really important role in cells in regulating METABOLIC PATHWAYS.
- These are a series of reactions, all catalysed by enzymes
- The PRODUCT made by the first enzyme is then used as the SUBSTRATE for the second enzyme.
- And so on down the pathway
End-product inhibition
- The process that requires the end product of the enzyme-catalysed reaction , may SLOW DOWN.
- This means LESS of the end-product is needed
- The rate of the metabolic reaction needs to be REDUCED to decrease the wastage of valuable resources.
- To do this the FINAL PRODUCT in the pathway ATTACHES TO & INHIBITS an EARLY STAGE enzyme.
- If the process rate INCREASES, more of the final product is used , so less of the final product is inhibiting enzyme 1
- So the rate of the metabolic reaction increases.
EXAMPLES of end-product inhibitors
AMINO ACIDS:
- needed when the cell is synthesising proteins
- If the rate of protein synthesis decreases, the amino acid made by the pathway inhibits and early stage enzyme, reducing the rate of the metabolic pathway.
ATP:
- the end product of respiration which is need to transfer energy around the cell
- Is the end-product inhibitor of an early stage enzyme in respiration.
End-product inhibition is an example of …
( two things)
NEGATIVE FEEDBACK:
- Used to keep the levels of key molecules withing a SET RANGE.
- If the range VARIES, the end-product inhibition brings the level back into range.
NON-COMPETITVE INHIBITION:
- Takes place through the allosteric site of the enzyme
Cofactors
- Many enzymes function in partnership with another chemical:
- COENZYMES ( Large organic molecules )
- relatively small molecules
- Prosthetic groups
COFACTORS ~ Relatively small molecules
EXAMPLE
Amylase
Starch + water ————————— maltose
CHLORIDE ION:
- Simple mineral ion
- Has to attach to the amylase molecule
- Without it, amylase cannot catalyse the
reaction - Cl- is not a substrate for amylase but is required for the reaction to occur
COFACTORS ~ Coenzymes
- Large , complex organic (contain carbon) molecules.
- Many come from VITAMINS we find in our diet
Example ~ NAD
- TEMPORARILY binds to many of the enzymes involved in RESPIRATION.
- Role is to transfer HYDROGEN atoms from one molecule to another
- Made from the VITAMIN NIACIN ( vitamin B3)
COFACTORS ~ Prosthetic groups
- PERMANENT PART of the enzyme structure
Example ~ ZINC ION
- CARBONIC ANHYDRASE catalyses the formation of carbonic acid from carbon dioxide and water
CO2 + H2O —————— H2CO3
- Carbonic anhydrase contains Zn2+ which is a permanent part of the enzyme structure
Metabolic poisons
- Many toxins exert their effect because they INHIBIT or INACTIVATE enzymes
Example ~ CYANIDE
- Potassium cyanide is highly toxic as it inhibits AERBOIC RESPIRATION
- KCN is hydrolysed to produce hydrogen cyanide which dissociates into H+ and CN-.
- The CN- ion bind irreversibly to an enzyme found in MITOCHODRIA , inhibiting the final stag of aerobic respiration.
