Enzymes Flashcards
What do we harness energy into?
ATP
What is the law of Thermodynamics?
where the behaviour of energy is governed by.
What is the 1st law of thermodynamics?
energy cannot be created or destroyed
What is the 2nd law of thermodynamics?
energy transfer or transformation is never 100% efficient.
Part of energy is lost
What is the ultimate goal of the universe?
to disorder (fall apart)
What does energy transfer do in the 2nd law of thermodynamics?
increases entropy(disorder) of the universe. That is why the universe is expanding due to the increase in disorder (entropy)
What is the 3rd law of thermodynamics?
the entropy of a perfect crystal (solid) at a temp of absolute zero degrees is zero.
Even though something is a solid object, its still made up of atoms held by bonds and those bonds are not static they are vibrating where they release potential energy in form of kinetic energy. Those vibrations stop when it reaches a temperature of absolute zero : which is -273.15 degrees Celsius.
How can you stop energy loss?
energy is always lost, only way to stop energy loss is to freeze everything.
What is entropy?
the universe tends towards disorder
What is an example of entropy occurring within our system which would cause to death?
e.g if we weren’t taking in food for additional energy, we would expel all that energy through by-product of metabolism as heat, we lose that through your systems and would die.
What is the relation between entropy and life?
Entropy and life have to be in a constant intricate balance with each other to survive.
Why does an organism need input of energy?
that means an organism to survive needs a constant input of energy otherwise you would succumb to entropy (disorder)
What does every organism/living cells do?
constantly producing heat as a by-product of metabolism- which means we are increasing entropy
How do we remain in balance when we lose energy as heat?
our ecosystem, have a constant input of energy from the sun, in the form of photons from light.
Constant balance, constant influx of energy in photons of light and constantly loosing as heat to environment which works into space.
Where else can we receive energy from?
Photosynthesising plants can harness these photons of energy and turn into molecules where we can extract energy from which works its way up into the system.
How do we not succumb to entropy?
constantly taking in food, metabolism breaks it down and harnesses the energy and traps in ATP that we can use
Why else do we lose heat from carbon dioxide and water?
in chemical bonds in carbon dioxide and water as we have to bond them together so its the potential energy we lose from our system.
What is free energy?
the energy in chemical reactions
How do chemical reactions occur?
spontaneously as its between only one molecule with another molecule- if they come together and collide and there is enough energy that energy can be transferred to a breaking of a bond or making a bond therefore have reactions occurring.
When does entropy favour a reaction?
to increase disorder within the universe (as it states in law of thermodynamics)-
How is a stable environment formed?
disorder will increase via if you have a little energy in a reaction but ultimately you get molecules which are formed (although the molecules that are formed have less energy they are still formed).
Why did spontaneous reactions became more efficient?
as the molecules formed helped reactions move forward.
What is the energy which allows a reaction to occur?
Activation energy
What is a.e?
free energy of activation which is the initial energy needed to start chemical reaction.
What else can trigger a reaction apart from activation energy?
thermal energy
What is the transition state?
where there is enough energy to make bonds
What do the products do when formed
and what is it known as?
release energy from system which is known as Gibbs free energy
What is the probability that the activation energy is reached spontaneously?
very low because your not directing any energy to make sure you have enough energy at a one time point to reach the transition state and have sufficient a.e.
How long would a chemical reactions take without anything?
chemical reactions let go on its own without proteins/enzymes or a.e would take hours
-this is how enzymes are evolved
What does an enzyme do in a chemical reaction?
enzymes co ordinate a chemical reaction which decreases a.e energy for the reaction to proceed.
What does the enzyme have no effect on?
Has no effect on the total energy released from that reaction.
What are enzymes
catalyse reaction
What does the enzyme-substrate complex do?
gives favourable conditions with less energy needed to put into the system to ultimately generate product and leave enzyme completely untouched.
How do enzymes speed up reaction rates?
by providing an alternative reaction pathway to lower activation energy
What are the enzymes made of?
proteins
What is the active site of an enzyme?
unique binding site making them specific catalysts for defined reactions.
What is an active site in a protein?
a cleft or a binding site in the 3D structure
What is a protein made of and what are the bonds it consists of?
tertiary/Quaternary structure- is a folded chain of a.a , all held in shape due to the h-bonds, ionic bonds and van der waals forces
What is a protein made of and what are the bonds it consists of?
tertiary/Quaternary structure- is a folded chain of amino acids , all held in shape due to the h-bonds, ionic bonds and van der waals forces
Why is the active site specific?
binding pocket/active site has a specific amino acid sequence (due to R groups)- creating a very specific hydrophobic or hydrophilic environment
different depending on the diff regions of binding pocket
How can a substrate bind to a enzymes active site?
if the chemical nature of binding pocket matches the chemical nature of the substrate.
What are some enzymes made of?
mix of a protein structure and contain (ribosomal) RNA strands i.e( ribosome)
What does the enzyme oxidoreductase do?
catalyse oxidation and reduction
What does the enzyme transferases do?
catalyse group transfer reactions, from one functional group to another
e.g amine group to another molecule
What does the enzyme hydrolases do?
catalyse reactions that involve hydrolysis
split large molecules into 2 using a water molecule
What does the enzyme lyases do?
catalyse reactions where functional groups are added to break double bond or where double bonds are formed from removal of functional groups
What does the enzyme isomerase do?
catalyse reactions that transfer functional groups within a molecule.
change structure of molecule however using the same building blocks
What does the enzyme ligases do?
catalyse reactions in which 2 chemical groups (substrates) are joined (ligated) due to condensation reactions. (remove water)
for e.g- in formation of chains of the building blocks such as monosaccharides to disaccharides
amino acids to proteins
How do enzymes make product?
enzymes modify the equilibrium of reaction- it does n
Why does the enzyme modify the equilibrium of a reaction?
as it forces the reaction to move in one direction
moves towards product side , makes more substrates into products and that how it modifies equilibrium
What can an enzyme not do?
increase the yield of the product from the same number of substrates
What is the limiting factor of yield
the number of substrates you put in enzyme
end up with the same amount
What does an enzyme do?
increases rate of production
How does an enzyme increase rate of production?
By reducing amount of energy for the reaction to proceed via a enzyme - stabilising the transition state
transition state is the highest a.e on a reaction
a.e is lowered when a catalyst is used - reaction takes less time to proceed
Once the transition state energy is reached a reaction will proceed to completion
What is the enzyme complementary to?
transition state , not to substrate in order to facilitate the reaction efficiently
What does the enzyme bound to the transition state accomplish?
it forces local bond tension or a conformational change that favours energy transfer.-
What is the conformational change of the shape of the enzyme?
as less energy is put in so requires less energy to break the bonds as the conformation of the enzyme is changed which is more complementary so you can introduce a little thermal energy to break bonds more quickly.
What is the lock and key model?
the shape of the enzyme active site and substrate fit together perfectly without conformational change.
What are the 2 shapes of the lock and key considered as?
rigid and fixed
fit in one orientation
What is the induced fit model?
binding of the substrate induces a conformational change in the active site of the enzyme.
The enzyme may also distort the substrate, forcing it into a conformation that is similar to the transition state.
Put strain on the the substrate, weakening the bonds that hold it together, reducing the activation energy
How reaction velocity rates change with varying substrate concentration?
when you increase amount of substrate, there is slow down of product being produced , concentration of enzyme becomes limiting factor.
What is maximum velocity?
saturated amount of enzyme, even though more substrate is added to solution you cant create more product
maximum rate of production is reached.
How is the extent of a product formed determined?
due to the function of time for a series of substrate concentrations
When is all product formed/ reaction equilibrium?
until a time is reached where there is no net change in the concentration of substrate or product.
What does the Michealis constant Km tell you?
tells you substrate concentration, at which half the enzyme is bound to the substrate
What is the reason why the Michealis constant Km tells you this?
it gives an indication of how well a substrate complexes with a given enzyme (how specific the enzyme is to the substrate)
indication of binding efficiency
How do we develop drugs?
need to generate a substrate with a higher binding affinity (than normal substrate which binds to an enzyme) as it needs to out-compete the other substrate which inhibits enzymes.
What does Small Km indicate?
indicates that the enzyme has a high affinity for the substrate, means you need low conc of substrate for the enzyme to be saturated
What does Large Km indicate?
the need for high substrate conc to saturate and the reaction to achieve maximum reaction velocity
Why is Km important?
if you want to inhibit enzymes in the body- a large number of drugs are enzyme inhibitors
How to inhibit enzyme?
competitive inhibition -
What is competitive inhibition?
where you generate an inhibitor which has the same molecular formula identical to active site of the enzyme which you want to block the function of. That means the inhibitor directly competes for the active site of the enzyme with the normal substrate.
Is the inhibitor permanent?
no its reversible, so can unbind and probability the next one which comes along is a substrate
What can the enzyme not do?
enzyme can not bind substrate or inhibitor at the same time which means you have an increase in your Km
What is the reason for the increase in Km?
to reach half velocity of reaction - you have to increase substrate conc so the probabilty the substrate will bind to the binding site active site there is a higher probability compared to inhibitor.
When will Km increase?
when you have a competitive inhibitor
What is required to reach maximum velocity and voids the inhibitor completely?
increased substrate conc required to reach maximum velocity as it can then out compete the inhibitor for binding
saturate the system with substrate to make the inhibitor void.
What can competitive inhibitors also be?
allostaric - when the inhibitor binds to another part of the enzyme (protein), which changes shape and blocks the binding site.- same kinetics
What is a non-competitive inhibitor?
inhibitor prevents conformational change in enzyme- the a.e not decreased
reaction occurs spontaneously
not sped up
Without an inhibitor?
doesn’t interfere with active site of enzyme
**binds somewhere else on enzyme
changes conformation - turns the substrate into the right conformation to reduce activation energy of the reaction
Is the inhibitor permanant in the non-competitive inhibition?
yes they are irreversible
As there
Why does non-competitive inhibitor have a constant Km?
due to decreased maximum velocity
because there is the same conc of enzyme and inhibitor, but there is an increase in substrate concentration , but as its not competing , the inhibitor will always be able to bind to enzyme , even if you increase substrate concentration.
In non-competitive inhibiton…
there is no competition for binding sites
no effect in increasing substrate conc
Why is the non-competivite inhibition irreversible?
because there is reversible binding of the inhibitor to an allosteric site and it cannot be reversed by adding more substrate
Why does the non-competitive inhibition differ from competitive inhibition?
because the binding of the inhibitor does not prevent binding of the substrate
How are enzymes regulated in 3 ways?
- Activation of zymogen
- Reversible Phosphorylation-
- Competitive product inhibition
What is activation of zymogen?
produces enzymes as proteins which are inactive and become activated once a portion is cleaved off (cut off) which exposes active site and bind to substrate.
What is reversible phosphorylation?
inactivate an active site of a protein by phosphorylating a amino acid- which changes conformation of active site and is inactive until it is dephosphorylated.
What is competitive product inhibtion?
the products of reaction feed back and inhibit and become inhibitors of enzyme- product of reaction can become inhibitor of that enzyme
What are zymogens?
inactive precursor enzymes (which means they are proteins)
region cleaved off by hydrolysis which reveals the active site- do this to enzymes which are pulling building blocks off life apart.
What are the reasons for it becoming inactive?
to prevent unwanted destruction of cellullar proteins
What is the zymogen for pepsin?
is the pepsinogen which is not activated until secreted from cells and the low pH environment
What do parietal cells secrete?
secrete HCL which decreases pH
