Lect 9. Energy & Metabolism - Enzymes Flashcards
What is an enzyme?
A catalyst or catalytic protein that speeds up the rate of a reaction without being consumed or altered by the reaction.
W/out enzymes, the pathways of metabolism would be too slow to maintain an organism’s biological needs
What is the state in which the reshaping of the starting molecule into a highly unstable state is involved?
the transition state
this happens before the reaction can proceed
The energy needed to reshape the reactant molecule is called:
the free energy of activation / activation energy Ea
Ea is often supplied in which form?
It is often supplied in the form of heat that the reactant molecules absorb from their surroundings. This thermal E increases the speed of the molecules, making them collide more and harder causing the bonds to break.
Ea provides a barrier that determines:
the rate at which a reaction will occur.
Heat speeds up a reaction by allowing reactants to reach the transition state more often. But why is using thermal energy inappropriate for biological systems?
- High temp denatures proteins and kills cells
- Heat would speed all the cells reactions, not just the necessary ones
Enzymes are very selective in the reactions they catalyze: they determine which chemical reaction will occur, when and where in the cell. What is the location on the enzyme at which the reaction occurs called? (Where does the substrate bind on the enzyme?)
Active Site
Enzyme + substrate(s) =
enzyme-substrate complex (temporary)
When enzyme and substrate join, catalytic action of enzyme converts S to product
Most metabolic reactions are reversible: an enzyme can catalyze both _____.
forward and reverse reactions
The capacity of an enzyme to catalyze both reactions depends on:
the concentration of both substrate and products
An active site is typically:
describe it
a pocket or groove on the surface of the protein formed by a few AAs
Substrate is held in active site mainly by:
bonding?
H-bonds and some ionic bonds
Interaction b/w substrate and the AAs of the protein cause the active site to fit more snuggly around the substrate. This is called:
induced fit
It brings chemical groups into position that increase chemical reaction rate.
The product leaves the active site and a new substrate enters.
How do enzymes lower the Ea? (4)
- provide template for substrates to come together in proper orientation (otherwise rely on random molecular motion)
- can stretch the substrate molecules toward transition state (bending and stressing critical bonds)
- can directly participate in the chemical reaction (often involves brief covalent bonding between an active site R-gr and the substrate)
- can provide a favourable microenvironment that is more conductive to a particular type of reaction (ex: active site composed of AA.s w/ acidic R-gr creates a pocket of low pH in neutral cell)
The rate at which an enzyme converts a substrate to a product depends on:
initial substrate concentration. The greater the [ ] of S molecules, the more frequently they come in contact w/ enzyme’s active site.
At a certain concentration, all active sites are taken up. This is the substrate concentration at which the enzyme is:
saturated.
At enzyme saturation, the rate of the reaction depends on:
how fast the active site can convert the substrate to product.
The cell can speed up the reaction rate by adding more enzyme molecules.
Optimal Enzymatic Conditions
Temperature: up to a point, the rate of an enzymatic reaction increases with an increase in temp, because:
there is an increase in collision of substrate molecules with enzyme molecules.
Most enzymes have an optimal pH ranging from
6 to 8
Optimal temperature and pH of an enzyme will vary on type of organism it is found in and where in the organism it is found. ex: lysosomes have a ____ pH
low pH. HCl help denature 4°, 3° and even 2° proteins.
Co-factors
Various types of chemicals can serve to promote or inhibit enzyme activity. Prosthetic groups or co-enzymes are:
inorganic or organic molecules that allow the enzyme to function properly. They can be bound tightly to the enzyme or they can bind loosely and reversibly.
A holoenzyme consists of:
- aa (protein) part of the enzyme called apoenzyme
- non-protein part called the cofactor
Terminology Summary
Simple Protein: made only aa
Conjugated Protein is also called:
holoenzyme
The aa part of a holoenzyme is called
the apoenzyme
If the cofactor of a holoenzyme is organic, it is a
co-enzyme
most vitamins
If the co-factor of a holoenzyme is inorganic, it is called a
prosthetic group
ex: zinc, copper, iron, magnesium
Regulating Enzyme Activity
In order to have a properly functioning cell, it must be able to tightly regulate its metabolic pathways. This is done, in part, by controlling when and where an enzyme is active. Achieved in 2 ways:
- switching on or off the genes that encode specific enzymes (gene regulation)
- regulating the activity of an enzyme once it has been synthesized (inactive enzyme when w/out an effector in allosteric site)
Once the enzyme has been synthesized, there are 2 ways to regulate its activity:
- Activation or Inhibition
- Feedback Inhibition
Often, molecules that regulate enzyme activity do so by acting like noncompetitve reversible inhibitors or activators. These reversibly bind to allosteric sites and either stabilize an enzyme in its active form (____) or deactivate it (____).
These reversibly bind to allosteric sites and either stabilize an enzyme in its active form (activators) or deactivate it (inhibitors).
An enzyme inhibitor is
any molecule that prevents an enzyme from functioning properly (inhibits catalysis).
ex: Penicillin blocks the active site of an enzyme used in the synthesis of bacterial cell walls
Inhibition of an enzyme activity can be irreversible if the inhibitor binds to the enzyme:
covalently.
Inhibition of an enzyme activity can be reversible if the inhibitor binds to the enzyme:
with weak bonds.
Differentiate competitive and noncompetitive inhibitors
competitive:
- resemble normal substrate of enzyme
- compete with substrate for the active site
noncompetitive aka allosteric inhibitors:
- do not directly compete with substrate for active site
- instead bind to the enzyme at another location (allosteric site)
- causes enzyme to change shape -> active site less effective
How can the competition between (competitive) inhibitors and substrate be overcome?
by increasing substrate concentration
Cooperativity is another form of:
allosteric activation
The binding of one substrate molecule to 1 active site may affect the other ones in the complex. One substrate molecule primes the enzyme to:
accept additional substrate molecules. It stimulates catalytic activity of the enzyme.
In feedback inhibition, a pathway is shut off by its own end-product. The end-product becomes the ____ to an enzyme that acts early in the pathway.
common method of metabolic control
The end-product becomes the inhibitor to an enzyme that acts early in the pathway.
ex: ATP can allosterically inhibit an enzyme involved in the ATP-generating pathway.
